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For a taxpayer, refunds are always pleasant and it is been looked upon as a blessing in spite of the fact what it really is the reimbursement of tax payers own money by the government. This factor brings it near to recovery of money loaned to a friend that you thought might never come back.

In every taxing statute administration of refund aims at providing prompt payments to the taxpayers in order to minimize the loss of interest to taxpayers and so is the case with GST. The article is an attempt to compile the common issues or errors faced by taxpayers in processing their refunds.

Under the GST regime, the cases of refund can be summarized as below, and evidently, they are mostly governed by Section 54 of CGST Act, 2017 and Rules 89/96 of CGST Rules, 2007

Refund under the GST regime


Provision of Law

Form of Application


Tax Outflow


Export of goods/services with LUT (without payment of Tax)

Rule 89rws Section 54 of CGST Act


Restriction on value to 1.5 of the value of domestic goods

The input of capital goods not allowed

Duty drawback of GST shall not be availed

Refund as per formula envisaged

0% on Supply

ITC and refund allowed

Export of goods with payment of tax

Rule 96 rws Section 54 of CGST Act

Shipping Bill deemed to be refund application

Validation of return data with shipping bill/EGM data on ICEGATE

Duty drawback of GST shall not be availed


Refund of IGST paid allowed

Export of Services with payment of tax

Rule 89rws Section 54 of CGST Act


Uploading of details related to export viz. invoices/BRC on portal

Duty drawback of GST shall not be availed


Refund of IGST paid allowed

Refund in case of supplies to SEZ/deemed exports with payment of tax

Rule 89rws Section 54 of CGST Act


Uploading of invoice details with relevant endorsement/declarations


Refund of IGST paid allowed

Refund in case of supplies to SEZ without payment of tax

Rule 89rws Section 54 of CGST Act


Refund as per formula envisaged

0% on Supply

ITC and refund allowed

Unutilized credit in case of inverted duty structure

Rule 89rws Section 54 of CGST Act


The input tax credit of services disputed

Refund as per formula envisaged

No refund on invoices not appearing in GSTR 2A

HSN/SAC wise summary of inward supplies required

Tax payable under same head (CGST/IGST/SGST)

Refund of excess credit allowed

Refund issues in Inverted Duty Structure

In the wake of conflicting judgments by the Gujarat High Court and Madras High court, the basic issue faced by taxpayers is whether or not to include the amount of unutilized ITC in respect of input services in their refund application.

Gujarat High Court in the case of VKC Footsteps India Pvt. Ltd. Vs. Union of India has declared that Rule 89(5) is ultra-vires to Section 54(3) of the CGST Act in as much as it debars the refund of ITC on input services. However, Madras High Court while deciding the issue in the case of Tvl. Transtonnelstroy Afcons Joint venture ruled out:-

"The extension of the benefit of refund only to the unutilized credit that accumulates on account of the rate of tax on input goods being higher than the rate of tax on output supplies by excluding unutilized input tax credit that accumulated on account of input services is a valid classification and a valid exercise of legislative power”

As per settled law decision of high courts are only applicable only to the relevant states and thus until and unless the issue is settled by the supreme court only recourse available to the taxpayers is to file a writ petition in the respective states in case the refund of unutilized ITC in respect of input services is sought.

Refund issues in Exports

Section 16(3) of the CGST Act, 2007 entitles a person making zero rated supply to claim a refund as per Section 54 of the CGST Act,2007 in the following two ways:-

  1. Claim refund of unutilized tax credit (aka rebate under LUT); or
  2. Claim refund of tax paid on exported goods (aka export without LUT)

In consonance with the intent of law Section 54 defines refund to include a refund of the unutilized input tax credit of every kind however Rule 89 governing form and manner of refund prescribes formula that includes only input and input services in net ITC and thereby exclude ITC in respect of capital goods.

Therefore the exporters are often in dilemma whether to include ITC of capital goods in refund application or not. To address the same circular no 18/18/2017-GST clarified that ITC on capital goods is not available under LUT option however the matter still can be contested legally using the rationale and analogy of ruling of Gujarat high court in the VKC Footsteps India Pvt. Ltd. Vs. Union of India.

Another common issue in refund faced by exporters is invoice mismatching i.e. details filed in Table 6A of GSTR-1 or GSTR-3B and Shipping Bill details on Customs EDI are not coinciding. Circular No. 42/2017 highlight errors noted at customs EDI and possible remedies as below:

Error Code





Invalid Shipping Bill Number

Amend details through Table 9 of GSTR-1 and enter the correct number


EGM not filed

The exporter may approach the Shipping Lines to file the EGM immediately. If EGM is already filed by shipping line correctly, the "Revalidate EGM” option may be used by EGM Officer


Mismatch of GSTIN in shipping bill and GSTR-1/3B where PAN provided in shipping bill is the same as that of GSTR-1

Submit undertaking at customs


Invoice already received and validated

Duplicated entry. Check shipping bill status on ICES


The amount of IGST paid is different in Shipping Bill and GSTR-1

Amend GSTR-1 and adjust the amount in GSTR 3B of the subsequent period

Ensure that admitted tax liability of IGST under table 3.1(b) of GSTR-3B(Exports), is equal to, or greater than, the IGST amount claimed to have been paid under Table 6A of GSTR-1 of the corresponding period


Incorrect Shipping Bill/ Invoice details in GSTR-1

Amend details through Table 9 of GSTR-1

Another common query is that what to do in a case where while filing a refund application an error as to amount has been committed but the application has been processed and the amount has been remitted in the bank account. The taxpayers shall bear in mind that the department can consider this as a case of erroneous refund and recover the same along with interest under Section 73. Therefore it is advisable that taxpayers should repay excess refund along with interest through DRC-03 and intimate proper officer in writing.

Refund application by SEZ units

As per section 54(3) read with Rule 89(1)(2) of CGST Rules,2007 in respect of supplies to a special economic zone unit or a special economic zone developer, the application shall be filed by the :

(a) supplier of goods after such goods have been admitted in full in the Special Economic Zone for authorized operations, as endorsed by the specified officer of the Zone;

(b) supplier of services along with such evidence regarding receipt of services for authorized operations as endorsed by the specified officer of the Zone:


Rule 89 further stipulates that a declaration to the effect that tax has not been collected by SEZ or SEZ developer shall be accompanied with refund application in cases of supply of goods/services made to SEZ unit or developer

Thus it can be inferred from above that SEZ unit or developers themselves cannot file a refund application even in case of unutilized tax credit where SEZ has made "Zero rated supply without payment of tax” and supplies have been procured from DTA vendors who have actually recovered tax from them which seems to be a bit absurd for the reason that allowing the supplier to claim a refund and not SEZ unit will result in increased cost & defy the objective of promoting exports. Although this view has been upheld by the honorable high court in the case of M/s Vaachi International India Private Limited the matter can be suitably contested at higher forums.


The author is a chartered accountant offering GST advisory & consultancy and can be reached at The views are strictly personal.


Published by

Chandani Nawalkha
Category GST   Report

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