Customs Clearance Fees and Procedures in India 2026

A shipment can be packed, booked, and ready at the port, yet still get held due to customs queries, unclear charges, or missing documentation. On average, export customs clearance in India takes nearly 23 hours at seaports, which can disrupt schedules and add unforeseen costs. Delays affect your overseas buyer, impacting delivery commitments and future orders.

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The solution lies in knowing exactly how custom clearance charges are structured, what drives them, and where exporters commonly make mistakes that trigger reassessment or delays. When you understand the procedures, documentation flow, and cost components in advance, you protect your shipment timelines and quote prices to buyers with greater confidence.

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This guide explores how customs clearance works in India in 2026, what fees exporters must account for, how those fees are calculated, and where exporters typically go wrong. 

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In a nutshell:

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• Customs clearance charges in India include government fees, broker charges, documentation costs, and handling fees, all of which impact shipment timelines and margins.
• Factors like HS code classification, FOB value, export duty, cargo type, and port of export influence total clearance costs and risk of delays.
• The customs clearance process involves AD code registration, shipping bill filing through ICEGATE, assessment, risk-based inspection, LEO issuance, and EGM filing.
• Accurate and complete documentation, including commercial invoices, packing lists, shipping bills, and regulatory certificates, is crucial to avoid reassessment, penalties, and indirect charges.
• Proactive planning, validation of HS codes, pre-export filing, buffer management, and staying updated with regulations can significantly reduce clearance delays and extra costs.

What are Custom Clearance Charges and Why It Matters

Custom clearance charges refer to the statutory levies and service-related fees payable when Indian Customs processes your export shipment. These charges must be settled before your cargo receives the Let Export Order (LEO), without which the container cannot be loaded onto the vessel.

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Customs clearance is not just a compliance step. It directly affects your commercial outcome:

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• Impacts your margin: Underestimating custom clearance charges can reduce your profit, especially in price-sensitive export markets.
• Affects buyer commitments: Clearance delays can push vessel cut-offs, leading to shipment rollovers and missed delivery timelines.
• Triggers avoidable penalties: Incorrect declarations may result in reassessment, fines, or extended scrutiny.
• Increases indirect costs: Delays during clearance often lead to storage, detention, or demurrage charges at the port.
• Creates communication pressure: If you cannot confirm clearance status confidently, buyer trust weakens.

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In the next section, we’ll examine what influences these charges in the first place.

Factors Affecting Customs Clearance Fees

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Several factors determine how much exporters pay for customs clearance, and most of these are within their control when properly anticipated.

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• HS Code Classification: The HS code determines duty applicability, compliance checks, and scrutiny level. Incorrect classification can lead to reassessment, examination, and added clearance costs.
• Export Duty Applicability: Certain goods attract export duty or cess. If not included in your FOB price, it reduces your shipment margin and may require price adjustments with your buyer.
• Declared FOB Value: Customs reviews whether the declared value reflects market reality. Under- or inconsistent valuation may trigger queries, delaying clearance and increasing indirect costs.
• Port of Export: Procedures differ across ports like the Nhava Sheva Port and the Mundra Port. Examination rates, workload, and scanning practices can affect your shipment timeline and fees.
• Export Incentive Claims: If you claim RoDTEP or duty drawback, documentation scrutiny increases. Errors or missing information can slow approval, delaying benefit realization and impacting cash flow.
• Cargo Type and Risk Category: Restricted, hazardous, or high-risk goods are more likely to be examined. Properly classifying cargo and providing accurate documentation can help reduce additional charges and port stay.
• Documentation Accuracy: Mismatches between the invoice, packing list, and shipping bill often result in reassessment. Even minor errors can delay your Let Export Order (LEO) and increase costs.

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Understanding these variables helps exporters estimate costs correctly and prevent unexpected revisions. Let’s now break down the types of fees you can actually encounter.

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Types of Customs Clearance Fees in India

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Custom clearance charges in India can be broadly categorized into government charges and service-related fees. You must understand the distinction to plan costs accurately.

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For exporters from India, the key types of charges you may encounter in the customs clearance process include: 

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1. Government-Imposed Charges

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These include:

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• Export duty (if applicable)
• Cess on specific commodities
• Customs processing fees

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Export duty applies only to certain goods, such as specific minerals or raw materials. Many manufactured goods have no export duty but still require formal clearance. 

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Exporters should confirm duty applicability before pricing contracts.

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2. Customs Broker (CHA) Fees

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A licensed customs broker files the Shipping Bill and manages clearance formalities.

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Their charges may include:

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• Filing Shipping Bills
• Document submission on ICEGATE
• Handling assessment queries
• Coordinating examination

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These charges may be structured per shipment or per container.

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3. Documentation and Processing Charges

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These include:

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• Shipping Bill filing fees
• Amendment charges
• Digital signature usage
• EDI processing fees

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Frequent amendments due to documentation errors increase overall clearance charges. Exporters can reduce costs by ensuring all documents are complete and accurate.

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4. Examination and Handling Charges

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If customs orders a physical examination:

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• Container destuffing and restuffing costs apply
• Labor charges increase
• Port handling charges may be levied

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Exporters with higher-risk cargo or incomplete documentation are more likely to incur these additional fees.

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5. Port and Terminal Charges Linked to Customs Delays

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While not directly government-imposed, delays in customs clearance can result in:

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• Container storage charges
• Ground rent
• Port demurrage

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These costs escalate quickly if clearance is not completed within the free time. Exporters should plan shipments to avoid delays and extra charges.

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Now that we’ve covered fee types, let’s examine how the customs clearance process works in India.

Customs Clearance Process in India

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The customs clearance process for exports follows a structured system under Indian Customs through ICEGATE. While the system is digitised, procedural accuracy remains critical.

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Here’s how export customs clearance typically works:

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1. AD Code Registration at the Port

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Before filing the shipping bill, your Authorized Dealer (AD) code must be registered at the specific port of export. This links your export proceeds to your bank and enables customs processing.

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What exporters should verify at this stage:

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• AD code is activated for the correct port
• IEC and bank details match customs records
• No pending discrepancies in ICEGATE

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If this step is incomplete, shipping bill filing cannot proceed. Many first-time exporters discover this only after cargo reaches the port, causing unnecessary delays and additional storage costs.

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2. Shipping Bill Filing Through ICEGATE

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The shipping bill is the official export declaration submitted electronically through ICEGATE. It contains the commercial and regulatory details of your shipment.

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Key information declared includes:

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• Exporter IEC and GST details
• HS code classification
• FOB value
• Scheme declarations (RoDTEP, drawback, etc.)
• Port and cargo details

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Errors at this stage are a common reason for reassessment. A mismatch between the invoice and the shipping bill can trigger clarification requests or shipment delays, affecting delivery commitments.

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3. Assessment by Customs Officer

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After submission, a customs officer reviews the shipping bill for classification accuracy, valuation correctness, and compliance with export regulations.

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During assessment, customs may:

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• Approve the shipping bill directly
• Raise queries for additional documents
• Mark the shipment for examination

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Delays often occur due to incorrect HS codes, undervaluation, or incomplete declarations. Exporters who track their shipping bill status can respond faster and prevent vessel schedule disruptions.

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4. Risk-Based Examination or Inspection

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Customs may select shipments for physical examination based on risk parameters, cargo category, or compliance history.

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If selected, the process typically involves:

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• Container opening
• Physical verification of goods
• Comparison with the invoice and the packing list
• Re-sealing after inspection

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Examination increases handling time and labour charges. If packing details do not match the declared information, extended checks may follow. Exporters should plan buffer time to avoid missing the vessel cut-off.

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5. Let Export Order (LEO)

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Let Export Order (LEO) is the final authorization from customs permitting the cargo to leave India. Without LEO, goods cannot be loaded onto the vessel.

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LEO is granted after:

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• Assessment clearance
• Completion of examination (if applicable)
• Payment of applicable duties or charges

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Exporters must confirm LEO status before assuming shipment readiness. Missing LEO can result in rollovers, affecting freight costs and buyer commitments.

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6. Export General Manifest (EGM) Filing

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After vessel departure, the shipping line files the Export General Manifest (EGM). This confirms that the cargo has officially left the country.

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Why exporters should track EGM status:

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• Export incentives depend on correct EGM filing
• Banking documentation references EGM data
• Incorrect EGM can delay incentives and financial settlements

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Even though EGM is filed by the carrier, exporters are responsible for verifying that shipment details match their records.

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Each of these stages plays a distinct role in customs clearance. Monitoring them proactively reduces the risk of unexpected delays and cost escalation.

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Let’s now look at the documents required in detail.

Documents Required for Custom Clearance Charges

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Proper documentation is key to managing custom clearance charges and preventing delays. Incomplete or inconsistent paperwork increases the chance of customs scrutiny and adds operational costs.

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Here are the core documents required:

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• Commercial Invoice: This must clearly state product description, HS code, FOB value, buyer details, and payment terms. If the description differs from the shipping bill or packing list, customs may hold the file for clarification.
• Packing List: Should include package count, net weight, gross weight, dimensions (if required), and marking details. Discrepancies between the packing list and port records often trigger inspection, which can delay clearance.
• Shipping Bill: Filed electronically through ICEGATE, this is the core customs declaration. Errors in HS code, scheme selection, or value declaration can lead to reassessment and delay in generating the Let Export Order (LEO).
• AD Code Registration Proof: Your Authorized Dealer code must be registered at the port of export. If not correctly activated, your shipping bill will not process, causing clearance delays.
• GST Details and LUT/Bond (If Exporting Without IGST Payment): If exporting under LUT, the declaration must align with GST filings. Incorrect tax declarations may result in queries and procedural delays for your shipment.
• Export Incentive Declarations (RoDTEP / Duty Drawback, if applicable): If you are claiming benefits, ensure the correct scheme code is selected in the shipping bill. Errors can delay incentive credit and increase follow-up work for you.
• Purchase Order or Letter of Credit (When Required): In certain cases, customs may request supporting transaction proof. Having buyer documentation ready avoids response delays that could affect shipment timing.
• Inspection Certificates (If Commodity-Specific):  Products such as food items, chemicals, or regulated goods may require additional certificates. Missing approvals can stop clearance entirely and increase costs.

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Accurate documentation reduces both direct and indirect custom clearance charges. Next, let’s examine how these fees are calculated.

How Customs Clearance Fees is Calculated in India

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Custom clearance charges are determined based on cargo value, applicable duties (if any), and service-related fees tied to processing and handling.

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Here’s how the calculation typically works:

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Step 1: Determine FOB Value
FOB Value = Invoice Value of Goods + Packing + Inland Transport to Port
This forms the base for any duty calculation. An incorrect FOB value can trigger reassessment or additional scrutiny.

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Step 2: Apply Export Duty (If Applicable)
Export Duty = FOB Value × Applicable Duty %
Most goods do not attract export duty, but certain restricted items do. Always confirm the current rate for your product category.

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Step 3: Add CHA (Custom House Agent) Fees
CHA Fees = Fixed Charges + Complexity Charges (based on cargo type, documents, and inspection)
These are service-based fees for processing and liaising with customs. They vary by shipment complexity.

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Step 4: Include Port and Handling Charges
Port Charges = Standard Handling Fee + Container Size Factor + Examination Charges (if applicable)
Charges vary by port, container size (20ft/40ft), and whether customs selects your cargo for inspection.

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Step 5: Account for Delay-Triggered Costs
Additional Charges = Demurrage + Storage + Detention (if clearance delays occur)
These are indirect costs that can increase total expenses if documentation or compliance issues cause delays.

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Example

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An exporter ships engineering goods with an FOB value of ₹25,00,000.

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• Export Duty: Not applicable
• CHA Fees: ₹12,000
• Port and Handling: ₹8,000
• Scanning/Processing: ₹5,000

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Total Base Custom Clearance Charges:
25,000 = 12,000 + 8,000 + 5,000

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If clearance is delayed and storage/demurrage of ₹6,000 applies:

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Effective Charges:  31,000 = 25,000 + 6,000

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This shows that even without export duty, indirect costs can significantly increase custom clearance charges, highlighting the need for accurate documentation and proactive timeline management.

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Now, let’s look at how exporters can reduce these costs and delays.

Tips to Minimise Customs Costs and Delays

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There are no shortcuts in customs, but you can adopt preparedness strategies to reduce unnecessary charges and procedural delays:

• Prepare Documents Carefully: Double-check every field in your commercial invoice, HS code, and shipping bill before filing. Mistakes here are the most common cause of rework and delays for exporters.
• Validate HS Codes Before Filing: HS codes determine tariff classification. Using the wrong code can trigger reassessment or hold your shipment at the port.
• Use Pre-Export Filing When Possible: Some ports allow filing shipping bills before cargo reaches the port. This can reduce on-dock waiting times and prevent missed vessel slots.
• Allow Buffer Time: Plan for the time between documentation filing, cargo arrival, and vessel cut-off schedules. Missing revised estimated departure (ETD) updates is a common cause of delay.
• Stay Updated with Regulation Changes: Customs procedures and fee schedules in India are updated periodically. Keeping informed prevents unexpected charges and procedural surprises.

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Preventing clearance issues requires coordination. This is where a structured logistics oversight partner like Pazago becomes important.

How Pazago Can Help Simplify Customs Clearance

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Custom clearance charges often increase when coordination gaps, documentation errors, or shipment visibility issues arise. Exporters need structured oversight across booking, documentation, and port coordination to prevent cost escalation.

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Pazago supports exporters through logistics-focused control that reduces procedural uncertainty.

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• Better Planning Around Custom Clearance Charges: Pazago helps exporters plan shipments with clarity on logistics timelines and related clearance stages, so cost forecasting remains accurate.
• Assured Container Booking and Loading Coordination: Customs delays can result in missed loading windows. Pazago coordinates container availability and loading schedules, reducing rollover risk when clearance is completed close to the cut-off.
• Ongoing Shipment Visibility Through Daily Updates: Once cargo is dispatched, exporters still need clarity on the status. Pazago provides daily shipment updates covering vessel movement and documentation progress. This helps exporters respond quickly if customs queries arise.
• Support for Exporters of All Sizes: Whether a first-time exporter managing one container or a large enterprise handling multiple shipments, Pazago provides structured coordination and consistent communication across the shipment lifecycle.

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By combining predictable freight planning with operational coordination, Pazago helps exporters reduce uncertainty during customs and transit stages.

Conclusion

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Customs clearance in India is not just a regulatory formality. It directly influences shipment timing, cost planning, and buyer trust. Understanding custom clearance charges, documentation requirements, and process flow helps exporters avoid preventable disruptions.

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 Preparation, documentation accuracy, and shipment visibility remain key to reducing risk. If you want more predictable export shipments, clearer visibility, and better control over customs-related disruptions, align your logistics planning with structured oversight and proactive monitoring.

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Work with Pazago to manage shipment timelines and customs coordination with greater clarity. Contact us today

FAQs

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1. How can you track the status of your customs clearance online?

You can track customs clearance status through the Indian Customs EDI system using your Bill of Entry or Shipment Reference Number. The official Indian Customs portal provides real-time updates on filing, assessment, examination, and release of goods, ensuring transparency throughout the import/export process.

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2. What penalties apply for non-compliance with customs procedures?

Non-compliance can lead to fines, seizure of goods, or prosecution under the Customs Act. Penalties depend on the severity of the violation, such as misdeclaration, undervaluation, or prohibited imports. Repeat offenses may result in higher fines or cancellation of import/export licenses.

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3. Are there any exemptions or concessions on customs duties in India?

Yes, exemptions exist under schemes like Advance Authorization, EPCG, and notifications for certain goods or sectors. Concessions may also apply for imports under Free Trade Agreements (FTAs) or for specific categories like raw materials, capital goods, or goods for export-oriented units.

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4. How is the basic customs duty (BCD) calculated on imported goods?

BCD is calculated as a percentage of the assessable value of imported goods, which includes cost, insurance, and freight (CIF). The rate depends on the product’s classification under the Customs Tariff Act and may vary for different categories, industries, or trade agreements.

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5. What is the Integrated Goods and Services Tax (IGST) in customs clearance?

IGST is levied on imported goods at the time of customs clearance, replacing both CGST and SGST for domestic taxation purposes. It is calculated on the sum of the assessable value, BCD, and other applicable duties, ensuring seamless tax compliance for imports.

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