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How to Check and Pay KRA Penalties

Edwin HindabyEdwin Hinda
June 28, 2025
Reading Time: 5 mins read
Are You A Taxpayer That Was Affected By The September 2026 Itax Disruption? Here Is What Happens Next Under The Kra'S Tax Procedures Act.

Kenyans at KRA offices in Mombasa. PHOTO/KEVIN ODIT.

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The Kenya Revenue Authority (KRA) charges penalties for different tax offences, including late filing of returns. 

For instance, KRA imposes a five per cent penalty of the due tax or Ksh2,000, whichever is higher, for late payment of individual returns.

On the other hand, failure to deduct Pay As You Earn (PAYE) attracts a penalty of 25% of the amount of the tax involved or Ksh10,000- whichever is higher, and an additional interest of one per cent per month until the payment is made.

For traders, failure to deduct or pay withholding tax is charged 10 per cent of the amount of the tax involved, up to a maximum of Ksh1 million

According to KRA, late filing of Monthly Rental Income (MRI) returns attracts five per cent of the tax due or Ksh2,000, whichever is higher, for individuals.

In addition, failure to file annual returns by non-individual taxpayers attracts 5% of the normal tax, or Ksh10,000. 

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Late filing of Excise Duty or VAT returns attracts a penalty of five per cent of the tax due or Ksh10,000, whichever is greater, while late payment of Excise Duty or VAT leads to a five per cent penalty on the tax due and one per cent monthly interest.


Also Read: KRA Rolls Out eTIMS System for Petrol Stations


How To Check for Penalties

  • Go to the iTax website, enter your KRA PIN to continue followed by your PIN/Password.
  • Type in the arithmetic sum of the security stamp to log in to your KRA account.
  • Once logged in, click on the menu tab ‘Debts and Enforcement”.
  • Click on Apply for a waiver for penalties and interests. Ensure you fill in all the required details.
  • After providing the details, click on the Apply for Waiver for Penalties and Interests then choose Applicant Type as; Taxpayer
  • Click on the Tax obligation, for example, Income Tax Individual.
  • Choose the type, either, penalty, interest, or both where applicable.
  • The system will display the total penalty that you owe on the screen.

Also Read: Everything You Need to Know About Filing Your KRA Returns as the Deadline Nears


How to Pay for KRA Penalty Online

  • Visit the iTax portal, enter the logging in credentials and solve the arithmetic prompt.
  • Navigate to the Payment menu, choose payment registration and click next.
  • Ensure you choose the correct category in the tax head, tax subhead section and the period.
  • You will see all the amount you owe KRA in the Liability Payment section.
  • Proceed to the Payment Details, choose the period you defaulted and the amount you want to pay.
  • Continue to the Payment Mode section and select the preferred payment modes.
  • Click the send button and download the electronic slip. The slip contains your ‘Payment Registration Number’ (PRN) which you will use as your account when paying via M-Pesa.
  • Go to your Mpesa and Select Lipa na M-Pesa.
  • Enter 572572 as the business number and the PRN as your account number.
  • Enter the amount you want to pay.
  • Put your Mpesa pin and click OK.

Follow our WhatsApp Channel and X Account for real-time news updates.

Kra Commissioner General Humphrey Wattanga Mulongo. Photo/ Kra. Customs Bond
KRA Commissioner General Humphrey Wattanga Mulongo. PHOTO/ KRA.
Tags: KRAKRA Penalties
Edwin Hinda

Edwin Hinda

This story was written by Edwin Hinda

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