How to Check KRA Penalties, Pay via Paybill 222222, or Apply for a Waiver

A penalty on iTax can come from a missed annual return, an unfiled monthly obligation or an unpaid tax balance. Before paying, identify the tax obligation, period and charge. A KSh 2,000 balance is not automatically the whole problem, and paying it does not file the missing return. This guide separates filing, payment, ledger correction and relief so you can deal with the actual cause.

KSh 2,000 is a minimum, not always a flat penalty

KRA’s published penalty guidance describes late individual income tax filing as 5% of the tax due or KSh 2,000, whichever is higher. A late individual Nil return commonly attracts the KSh 2,000 minimum because there is no tax due in the return. For companies, the late income tax return penalty is 5% of tax due or KSh 20,000, whichever is higher. Do not describe these as fixed amounts for every taxpayer.

VAT late filing is 5% of tax due or KSh 10,000, whichever is higher. Monthly Rental Income late filing is not automatically KSh 10,000 for everyone: KRA’s MRI guidance distinguishes individuals and companies, with the applicable 5% test and minimums of KSh 2,000 and KSh 20,000 respectively. A missed monthly return may create a separate late-filing charge for that period. This is different from a general KSh 10,000 monthly bill.

Late payment can also attract a penalty and interest in addition to late filing. Read each ledger entry rather than treating the total as one charge. Rules and historical assessments can depend on the period, obligation and taxpayer type. If an entry looks incorrect, obtain a statement and ask KRA to explain or correct it before creating a payment against the wrong period.

Check your filing history and outstanding ledger

1. 1Sign in yourself at https://itax.kra.go.ke. Never give an assistant your password, reset link or one-time code.
2. 2Review your registered tax obligations. Note the start date of each obligation; do not assume every tax applies simply because you have a PIN.
3. 3Open the available return-consultation and account or ledger enquiry screens. Download records of filed returns and outstanding assessments.
4. 4List each missing year or month, the relevant obligation, the reported tax and the penalty or interest. Keep payment receipts alongside the statement.
5. 5Check for payments already made but allocated to another period. These need reconciliation, not necessarily another payment.
6. 6Make a plan for returns, tax payments and any disputed entries separately. Deal with the earliest outstanding period first so the record stays organised.

How to file several years of unfiled Nil returns

Begin with the earliest outstanding year and work forward. This makes it easier to match acknowledgements and penalties, but it does not mean you should file Nil for every year. Check whether you had salary, business or rental income in each period. A student who later started employment may need Nil for one year and a normal income return for another.

1. 1Build a year-by-year list from the obligation commencement date and filing history. Mark years already filed so you do not duplicate them.
2. 2For the earliest year with genuinely no income to declare, choose Returns then File Nil Return and confirm the correct individual income tax obligation.
3. 3Enter or verify the return period shown by iTax. Read the declaration carefully and submit only when Nil is true for that year.
4. 4Download the acknowledgement and record the receipt number against that year. Move to the next missing year and repeat the checks.
5. 5Where income existed, stop and prepare the appropriate normal return with supporting records. Do not use Nil to avoid finding a P9 or business records.
6. 6Review the ledger again after filing. Outstanding tax, penalties or interest may remain even though all returns now show as submitted.

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Generate a Payment Registration Number before M-Pesa payment

A Payment Registration Number, or PRN, connects a payment to the selected tax liability. Your KRA PIN is not a substitute for the PRN in the M-Pesa account field. Use the number on the generated payment slip, and review the obligation, period and amount before paying. An incorrectly allocated payment can leave the original charge outstanding.

1. 1In iTax open Payments, then Payment Registration. Select the applicable tax head, subhead and payment type using the current screen labels.
2. 2Choose the correct period and assessed liability. Confirm whether you are paying tax, penalty or interest; do not choose an unrelated obligation to make the slip generate.
3. 3Generate and download the payment slip. Confirm the amount and copy the PRN exactly.
4. 4Open M-Pesa Pay Bill, enter KRA Paybill 222222, and use the generated PRN as the account number. Confirm the recipient and amount before authorising payment on your own phone.
5. 5Keep the M-Pesa confirmation and payment slip. Do not share your M-Pesa PIN or authorisation codes with anyone.
6. 6Check iTax for allocation after processing. If the payment does not appear against the intended liability, raise a reconciliation request with the receipt rather than immediately paying twice.

Waiver and amnesty are different

An amnesty is a time-limited statutory programme with specific eligible periods and conditions. KRA’s current 2026 programme runs from 1 July to 31 December 2026 and covers qualifying interest, penalties and fines for tax liabilities up to 31 December 2025. It does not cover liabilities arising from 1 January 2026. Where principal tax remains, the qualifying principal must be fully paid by 31 December 2026. A payment plan does not extend that deadline.

KRA instructs taxpayers with unfiled returns for periods up to 31 December 2025 to file them during the amnesty window. Qualifying Nil returns with no principal tax outstanding receive automatic late-filing penalty relief. Where filing establishes principal tax, that qualifying principal must also be fully paid within the programme deadline. Check the iTax ledger after processing; do not confuse automatic relief under the programme with approval of an unrelated waiver letter.

A waiver request is also not a guaranteed cancellation. The legal route and eligibility must be checked with KRA for your circumstances. An old iTax waiver menu or a persuasive letter does not establish that a current waiver power applies. Where a charge was wrongly raised, a correction or objection may be the appropriate route instead. Act promptly if an assessment notice gives an objection deadline.

Prepare an evidence-based request where KRA confirms a route

• Identify your PIN, obligation, exact periods, assessment references and the amount you are asking KRA to review.
• Explain the facts in date order. State the real reason for the missed filing or incorrect charge rather than copying a hardship story that is not yours.
• Attach relevant acknowledgements, payment receipts, correction records and evidence supporting your explanation. Keep unrelated medical or personal information out unless required.
• State the action requested: ledger correction, review of an assessment, or consideration under the specific relief route KRA has confirmed.
• Use the official channel KRA directs you to. If an iTax application is available for your case, upload the signed request and supporting documents in the permitted format.
• Save the submission reference and follow up using that reference. Do not assume a pending request has cleared the debt or unlocked a TCC.

Next step: clear the compliance blocker

Cyber Kenya can help you organise missing returns, interpret the displayed entries and prepare the right request. Use the KRA service link or WhatsApp button below and describe the tax year and error first. Official tax and penalties are separate from our assistance fee. Only KRA can confirm a correction, relief decision or certificate outcome; do not pay anyone promising automatic penalty deletion.

Official references

Use https://www.kra.go.ke for the current Offences and Penalties, Monthly Rental Income and Tax Amnesty guidance. Generate payment slips only through https://itax.kra.go.ke. Recheck current relief announcements and the period-specific assessment before deciding what to pay or request.