Introduction to VAT Mismatches in Kenya

Fixing VAT mismatches on iTax doesn’t happen through a special button or a complicated menu path. Instead, the Kenya Revenue Authority (KRA) uses a VAT Auto Assessment (VAA) process that notifies both the buyer and the seller of any inconsistencies. The correction happens through the normal VAT amendment process, and whichever party declared incorrect details must revise their VAT return to match the accurate transaction.

Here is the accurate, verified, and simplified explanation of exactly how and where VAT mismatch corrections happen on iTax:

Where You First See the VAT Mismatch – Email & iTax Notification

When a mismatch occurs, KRA automatically sends an Inconsistency Report to both parties:

• The buyer (who claimed input VAT)
• The supplier (who declared output VAT)

This report is sent to the registered email on iTax and contains:

• Supplier PIN
• Buyer PIN
• Invoice number
• Invoice date
• VAT amount
• Taxable value
• The nature of the mismatch

This is your first point of reference before logging into iTax.

What You Do First: Confirm the Correct Invoice Details

Before logging in, both parties must agree on:

• Correct invoice number

• Correct invoice date

• Correct taxable amount

• Correct VAT amount

• Correct supplier PIN

KRA requires the party whose entry is wrong to correct their return.
This ensures both sides of the transaction match perfectly.

Where on iTax You Actually Fix the Mismatch — The Amended Return Section

To correct the mismatching entry, log into your iTax account and proceed to the VAT return amendment area.
Unlike old guides that list long menu paths, the real and verified location is within the amended return workflow.

✔ How to Fix the Mismatch

1. Log into your KRA iTax account.

2. Go to the section labelled “Amend Return” or “File Amended Return.”

3. Select VAT (Value Added Tax).

4. Choose the tax period where the mismatch occurred.

5. Update the correct invoice details.

6. Ensure the details match the other party’s corrected declaration.

7. Submit the amended return.

This is the only official way mismatches are corrected in iTax.

When the Other Party (Supplier or Buyer) Must Amend

If the mismatch originates from someone else—for example:

• The supplier failed to declare your invoice

• The amounts they declared do not match your claim

• They entered the wrong invoice details

Then they must amend their VAT return—not you.

Once they file their amendment, your mismatch will automatically clear after the iTax system synchronizes the data.

How to Confirm That the Mismatch Has Been Successfully Resolved

After both sides correct their returns:

• Check your email for a follow-up notification

• Log back into iTax

• Open the VAT Auto Assessment or Inconsistency Report section

• Confirm that the invoice no longer appears under mismatches

• Check your VAT ledger for updated entries

If the mismatch remains, it may be due to:

• The supplier not submitting their amendment

• A second mismatch in the same invoice

• A timing delay in the iTax system

• An error requiring KRA support

What to Do If the Error Persists or the Supplier Is Uncooperative

KRA allows taxpayers to escalate unresolved mismatch issues through:

✔ KRA Contact Centre

Call for real-time guidance on VAT discrepancies.

✔ KRA Tax Service Offices

Visit your nearest KRA office for assisted amendments.

✔ Huduma Centre KRA Desk

Get help with VAT corrections and return amendments.

Failure to correct a mismatch within the timeline stated in the inconsistency notice can lead to:

• Disallowed input tax

• Additional tax assessments

• Penalties and interest

• Compliance rating downgrades

Use the iTax Invoice Checker Tool to Avoid Future Mismatches

To prevent similar issues, always validate invoices before filing VAT returns.

The iTax Invoice Checker Tool helps you confirm:

• Supplier PIN validity

• Invoice structure

• Invoice authenticity

• Matchability within the same tax period

This tool greatly reduces the risk of future VAT-related inconsistencies.

Penalties and Risks of Ignoring VAT Mismatches

If you do not fix mismatches:

1. Auto Assessments

KRA automatically taxes you for the disputed input VAT.

2. Interest Charges

1% per month.

3. Compliance Rating Impact

Poor ratings affect:

• Tenders

• Tax clearances

• Business licensing

This is why learning how to fix iTax VAT mismatches is essential.

How to Prevent Future VAT Mismatches in Kenya

Monthly Reconciliation Checklist

• Verify supplier PINs via the KRA PIN Checker

• Confirm invoice numbers and dates

• Request monthly supplier statements

• Reconcile before the 20th of every month

• Use eTIMS-compliant invoicing

How eTIMS Helps Reduce Mismatch Errors

• Auto-captures invoice data

• Eliminates manual entry mistakes

• Ensures supplier declarations match buyer claims

FAQs About How to Fix iTax VAT Mismatches

1. How fast can a VAT mismatch be fixed?

Within minutes if corrected on your end. Up to 72 hours if the supplier must amend their return.

2. Can I fix mismatches from previous years?

Yes, as long as the period is still open for amendment.

3. What if my supplier refuses to amend?

You must reverse the input VAT; otherwise KRA will penalize you.

4. Does eTIMS stop VAT mismatches completely?

It reduces them by over 90%, but supplier non-compliance can still cause mismatches.

5. Can a mismatch affect my tax compliance certificate?

Yes—unresolved mismatches affect your rating.

6. Will KRA block my PIN for mismatches?

Not immediately, but repeated non-corrections increase risk.

Conclusion

Understanding exactly how to fix iTax VAT mismatches helps Kenyan businesses stay compliant, avoid penalties, and maintain accurate tax records. With the right steps—reviewing your entries, communicating with suppliers, and amending returns—mismatches can be resolved quickly and confidently. Using eTIMS and monthly reconciliations will prevent future errors and protect your compliance standing.

Ready to Fix Your VAT Mismatches the Right Way?

Don't wait until KRA issues penalties, auto-assessments, or compliance warnings. Get professional support from experienced Kenya tax experts who handle VAT reconciliations, iTax amendments, and supplier mismatch resolutions every single day.
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