Issues Faced While Filing GSTR 9 and GSTR 9C

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Towards Goods and Services Tax (GST) compliance in India, businesses are seldom observed struggling with the complications of filing returns. These businesses can benefit from the two extremely significant elements of the GST standard, GSTR 9 and GSTR 9C. They are capable of eliminating any discrepancies and ensuring reliability in the annual financial reporting mechanism. This GSTR 9 filing guide presents you with the mainframe of GSTR 9 filing, highlighting the common issues businesses generally face while dealing with the same.

Understanding GSTR 9

GSTR 9 signifies the Annual Return as an integrated summary of the inward supplies collected and outward supplies forwarded within a financial year by an authorized taxpayer. It incorporates the use of a document that gives direct insight into a taxpayer’s financial actions and operations for the year. It is applied to both general and composition taxpayers, non-inclusive of casual taxpayers, Input Service Distributors (ISD), and uninhabitant taxpayers. Have a look at the key elements of the GSTR 9 document.

Part I: Basic Information

The section asks the taxpayer to fill in the general details like the legal name, business name, GSTIN, and the economic year concerning the return filing.

Part II: Details of Inward and Outward Supplies

For this, a very precisely detailed account is needed regarding the outward and inward supplies, classified as B2B, B2C, and exports. 

Part III: Details of ITC (Input Tax Credit)

The sections is concerned with a holistic report and information on the input tax credit acquired within a given year, with a peek of insights about ineligible credits. 

Part IV: Details of Tax Paid

Here, the taxpayers must disclose their GST creditworthiness and payments encountered during the financial year under heads: central, state, or integrated tax or cess.

Part V: Particulars of Demands and Refunds

This section will include any demands made, repayments, or reimbursements claimed for the given financial year.

Also Read: What is GSTR-9?

Common Challenges in GSTR 9 Filing

Get some quick details and understanding of the GST-related challenges to cut down on the complexities that arise during the filing process, streamlining the process and reducing errors. 

1. Inaccurate Reporting of Transactions

It is one of the significant issues faced in the GSTR 9 form. To make this a convenient process, businesses need to correctly categorize their inward and outward supplies, getting them reported to avoid errors.

Stick with sound and reliant accounting systems and a consistent reconciliation process that monitors transactions properly for the year. 

2. Reconciliation Issues in Input Tax Credit (ITC)

Businesses might deal with complications for availed and employed ITC when reconciled. If there is any discrepancy found, it could directly lead to extra compliance charges and penalties.

Assure regular reconciliations between GST returns and books of accounts to understand and eradicate any errors meticulously.

3. Lack of Documentation and Audit Trails

An unorganized audit trail and insufficient documentation negatively affect the flow of business, making it challenging to validate the information received in the GSTR document.

Keep intact the records and history of overall transactions, invoices, and relevant paperwork for a smooth and unhindered audit trail regarding GSTR 9 filing.

4. Ignorance of Amendments and Corrections

Non-abidance issues can result when businesses brush aside the significance of making changes and rectifications in the GSTR 9 form.

Maintain awareness of any amendments made in the GST regulations and carefully adjust those in the GSTR 9 filing to cut down on penalties.

Also Read: Challenges and Best Practices for GSTR-9 filing

5. GSTR 9C Mistakes to Avoid

1. Inadequate Reconciliation

There can be abnormalities and non-compliance if any business is incapable of reconciling the data in GSTR 9 with the inspected financial records. You can ensure a sufficient reconciliation process while investing time and provisions, assessing that all figures conform with the audited statements.

2. Lack of Auditor Certification

For a GSTR 9C document, you need accreditation by a CA. Bypassing this mandatory practice will result in non-compliance. Before you submit the GSTR 9C document, appoint a certified professional to get it certified.  

3. Incorrect Reporting and Additional Liabilities

Additional obligations could go unreported if businesses overlook their necessity during the audit procedure, which is responsible for improper financial reporting. Comprehensively review all the audited statements to discern the liabilities and include them appropriately in the GSTR 9C form.

Guide to Filing GSTR 9C

GSTR 9C has emerged as an important document encircling the navigation of companies through delicacies of Goods and Services Tax (GST) compliance measures. The document covers the space between annual returns and audited financial records for a given year. Check out the briefly described, influential guide to filing GSTR 9C and gain an understanding of the practical tips to optimize the process. 

1. Understanding GSTR 9C

GSTR 9C is also termed the Reconciliation Statement. It is the linkage ensured between annual returns (GSTR 9) and the examined financial records of an individual taxpayer. It is an obligation for companies surpassing the INR 2 Crores turnover. 

2. Key Components of GSTR 9C

  • Reconciliation Turnover: Companies are requested to reconcile the turnover included in the audited statements with the turnover assessed in the annual return of the GSTR 9 form. Any mismatch must be mediated.
  • Reconciliation for Taxable Income: This is the reconciliation of the taxable income declared in the GSTR 9C (audited statements) with the income verified in the GSTR 9 (annual return). Any changes must be inspected and rectified. 

3. Reconciliation of Input Tax Credit (ITC)

GSTR 9C asks businesses to match up the tax credit they claimed in their financial statements with what they said they got in their yearly return. If there are any differences, they need to figure out what went wrong and fix it.

4. Reconciliation of Tax Paid

Making sure that the amount of taxes you pay matches up with what you declare in your yearly tax report (called GSTR 9C) is super important. It’s like double-checking that the money you said you paid as taxes during the year lines up exactly with what your official financial records show. This step helps make sure everything adds up and is correct.

Also Read: How to file GSTR 9C Offline utility – General issues faced and how to solve them

Steps to File GSTR 9C Effectively

1. Engage a Qualified Auditor

Alright, so GSTR 9C says you need a certified accountant, like a chartered accountant or a cost accountant, to check things. Having a qualified auditor makes sure everything matches up properly and follows the right accounting rules.

2. Through Reconciliation Process

The real key to GSTR 9C is making sure everything matches up perfectly. Businesses need to spend effort and money to carefully check and compare their audited financial statements with

the yearly return. This means leaving no room for any differences or mistakes between the two.

3. Documentation is Key

Imagine your money is like a secret diary, but instead of writing about your day, it keeps track of every cent that comes in and goes out. This diary isn’t just for fun; it’s super important because it helps you figure out if everything adds up and helps prove where your money went if someone asks. So, jotting down all the money stuff, like receipts and papers, is key. It’s like making a trail of breadcrumbs so you can find your way back if needed.

4. Timely Filing

Make sure you file that GSTR 9C thing on time, or else you might get slapped with penalties. It’s like showing how serious your business is about following the GST rules. So, get it done before the deadline to stay out of trouble!

Common Pitfalls and Challenges in GSTR 9C

GSTR 9C is super important for keeping up with GST rules, but lots of businesses face problems when they try to file it. Knowing about these issues is key to fixing them and making sure everything goes smoothly when you’re doing the filing.

A. Incomplete or inaccurate Reconciliation

Problem: Sometimes, businesses have trouble making sure all their numbers match up correctly.

This can make the official money reports not quite line up with what they’re doing.

Solution: To fix this, they can use really good accounting software and special tools. They need to regularly check and compare all their numbers to catch any mistakes and fix them quickly.

B. Lack of Auditor Certification

Challenge: Some companies might forget that they need an auditor who’s certified for GSTR

9C, which could mean they aren’t following the rules properly.

Solution: Get a good auditor who knows a lot about GST rules to make sure they sign off on the statement that checks everything matches up before sending it in.

C. Failure to Disclose Additional Liabilities

Challenge: When audits uncover hidden debts or responsibilities, it can make the financial reports wrong.

Solution: Carefully check the audited money documents to find any extra debts and make sure

to tell about them correctly in GSTR 9C.

D. Non-disclosure of Unclaimed Input Tax Credit

Big Problem: If you forget to mention the unclaimed input tax credit from last year, you might end up facing fines.

Fix It: Look closely at your financial papers to find any leftover input tax credits and make

sure, it’s correctly included in GSTR 9C.

E. Ignoring Auditor’s Recommendations

Challenge: Sometimes, businesses ignore or forget the advice given by auditors when filing GSTR 9C, causing repeated problems with following the rules.

Solution: To solve this, businesses should quickly follow the suggestions given by auditors. This shows they’re serious about fixing any problems found and making sure the accounts match up properly.

Tips and Best Practices for Filing GSTR9 and GSTR 9C

As companies get set for their yearly GST dance, getting the hang of filing GSTR 9 and GSTR 9C becomes super important. So, here’s the lowdown on some helpful content on filing GSTR 9 tips and GSTR 9C reconciliation steps to make sure you breeze through filing without tripping up.

A. Start Early and Plan Strategically

GSTR 9 Filing Tip: Start getting everything ready to file GSTR 9 well before the deadline. This means collecting and sorting all the needed information early so that you don’t have a rush at the end. Doing it this way helps make sure everything’s accurate.

Steps for GSTR 9C Reconciliation: Start comparing your financial statements and annual returns early. This gives you plenty of time to carefully check and match everything up properly.

B. Maintain Accurate Records Throughout the Year

Keeping GSTR 9 on Track Tip: Keep really good records to make sure your reports are accurate.

Update your records often, especially when you need to fix mistakes or add new transactions.

Steps for GSTR 9C Reconciliation: Good records are super important for making sure everything matches up correctly. Regularly check and compare your transactions to avoid mixups between your financial statements and the yearly return form.

C. Leverage Technology for Data Management

For GSTR 9 Filing: Use computer programs or apps that handle money stuff to make your work easier. They can catch mistakes and help you work faster.

GSTR 9C Reconciliation Steps: Get tools that can compare different money records. They’ll help you find mistakes between what you say you earned and what you earned. These tools make it easier to fix and mix up.

D. Stay Informed About Regulatory Changes

Tip for Filing GSTR 9: Keep yourself updated with any new GST rules. Following the latest guidelines helps you follow the rules and avoid getting fined.

Steps for GSTR 9C Reconciliation: When rules change, it affects how we match things in GSTR 9C. Stay in the know and adjust how we match stuff to fit the new rules.

E. Engage Qualified Professionals

Filing GSTR 9 Tip: Getting help from tax experts or consultants can help when dealing with the complexities of GSTR 9. They know the ins and outs and can make sure everything is accurate and follows the GST rules.

GSTR 9C Reconciliation Steps: Bringing in a skilled auditor who knows a lot about GST rules is super important here. They’ll help double-check all the numbers to make sure they match up right and meet all the certification rules.

F. Regularly Reconcile Input Tax Credit (ITC)

GSTR 9 Tip: Make sure to check and match your tax credits regularly. This helps avoid mistakes when claiming credits in your yearly tax return.

Steps for GSTR 9C Reconciliation: It’s super important to carefully compare the tax credits in your financial documents with what you report in your annual tax return. This helps fix any differences or mistakes you might have made.


Filling out GSTR 9 and GSTR 9C might seem tricky, but if businesses take charge early and plan smartly, it becomes much easier. Following the tips and best practices shared here doesn’t just make filing simpler; it also helps in following GST rules better.

Getting things right with taxes can be a big puzzle, but there are some key moves to make it less of a headache. Starting early, keeping good records, using tech smartly, staying updated, getting help from the right experts, and making sure your numbers match up with the tax department’s records are super important. These steps can help businesses deal with the complicated GSTR 9 and GSTR 9C forms without stress, making sure everything is clear and follows the rules.

Paying attention to compliance isn’t just about following rules—it’s a chance to show how transparent your finances are and how committed you are to doing things right in business.

Keep yourself updated, take action ahead of time, and make filing GST taxes super smooth.


1. What is GSTR 9?

For a given year, GSTR 9 holds the annual account of an individual taxpayer’s financial transactions. In simple terms, GSTR 9 is a report that businesses have to fill out every year for the government. It shows all the buying and selling they did regarding taxes in a year. It’s a way for them to give a complete picture of their financial activities related to GST in one go.

2. What are the key components of GSTR 9?

The key components of GSTR 9 are namely; general information, details of supplies, input tax credit, tax reimbursement, and refund elements.

3. What are the common challenges in GSTR 9 filing?

Issues involve ITC reconciliation errors, improper reporting, and insufficiency of documents.

4. What is GSTR 9C and who files it?

GSTR 9C assists in resolving annual returns and approved financial statements for companies with turnover of over INR 2 Crores. So, if you’re a normal taxpayer or a company paying taxes regularly, except for some specific types like those who don’t do business all the time, those handling tax distributions, or those not living in the country, you’ve got to file GSTR 9.

5. What are the key components of GSTR 9C?

Coordination for turnover, taxable wages, input tax credit, and tax disbursed.

6. Why is auditor certification significant in GSTR 9C?

Auditor certification passes the precision and compliance checks necessary for GSTR 9C filing.

7. What are the common pitfalls in GSTR 9C filing?

Deficient reconciliation, insufficient certification, and non-disclosure of indebtedness are the common pitfalls in the GSTR 9C filing process.

8. Why is early planning crucial for GSTR 9?

Proper and timely planning helps ensure aligned information gathering cutting down on the risk of mistakes in GSTR 9 filing.

9. How can businesses use technology for GSTR 9?

Businesses can employ accounting applications and tools for effective and rapid reconciliation in GSTR 9 filing.

10. Why is staying informed about regulatory changes essential for GSTR compliance?

Staying updated and informed about regulatory alterations helps you conform with the latest GST regulations ultimately reducing the risk of penalties. 

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Saayak Karmakar Resident Editor
Hi, I am Saayak Karmakar. I am a freelance content writer with 7 + years of experience. I did my master's in mass communication from Guru Jambeswar University.

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