I paid CRA, but the payment went to the wrong account. What should I do?

Arsen Accounting Services · Question 105 · Sources checked October 29, 2026

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A payment can reach CRA yet sit in the wrong year or program account. Before paying again, find the transaction and confirm its destination. Keep the bank confirmation because it can help establish the amount, payment date, and account used.

Check processing and allocation

CRA advises allowing processing time before checking a payment: its guidance currently lists three business days for online payments and longer for mailed payments. In your CRA account, review both the intended balance and any available or unallocated payments.

Some transfers can be made through CRA's online services. Others require a transfer request or contact with CRA. Corporate income tax, payroll, and GST/HST have separate program accounts, even when they share the same business number.

Official guidance: [1].

An example worth catching early

A business owner pays a corporate balance using the GST/HST banking payee. The bank shows a successful payment, but the corporate account still shows arrears. The next step is to locate and transfer the payment, rather than treating the bank confirmation alone as proof that the corporate balance is cleared.

Prepare a payment-tracing package

• Payment amount and bank transaction confirmation.
• Date sent and the banking payee selected.
• Account or tax year that received the payment.
• Intended account, period, and assessment being paid.

Retain the transfer request reference and verify the corrected account once processed. Review any remaining interest or penalties rather than assuming they disappear automatically. If a deadline is close and the payment cannot be located, contact CRA with the evidence and ask what action is needed for that specific account. Avoid repeated transfers without first checking the earlier request.