Your CRA statement says you owe money you already paid. Here's how to find it

Summary

A statement of account from the Canada Revenue Agency (the CRA) is a running history of one of your corporation’s tax accounts: payments received, tax charged, interest added, and the balance left at the end of each period. A period is one stretch of time the account gets settled for, which for corporate income tax is one of your corporation’s fiscal years. A notice of assessment is a different document, carrying the CRA’s decision on what your corporation owes for a year. You can challenge that decision by filing a notice of objection within 90 days of the day the CRA sent the notice, or later on an application to extend the deadline by up to a year.¹ A statement holds nothing to object to, since it only reports what already happened in the account.

If a statement shows a balance you’re sure you paid, work through it in this order:

1. Wait for the payment to post, meaning for the CRA to record it against your account, which happens days after your bank shows the money leaving. Allow three business days for an online payment, or ten plus mailing time for a cheque, before you check, and five before you phone.²
2. Read back the payee you picked in online banking and the account number you typed.
3. Sign in to My Business Account, the CRA’s online portal for businesses, and look through your corporation’s other CRA accounts. The CRA keeps one for corporate income tax, one for GST/HST and one for payroll, and a payment can land in any of them.
4. If it landed in the wrong period, or in the wrong account under the same nine-digit business number that identifies your business to the CRA, move it back yourself. The correct account looked unpaid while your money sat elsewhere, so the CRA charged daily interest on it. A transferred payment keeps its original date, so that interest gets recalculated and comes off.³
5. If it went to a different business number, or to your own social insurance number, pay the correct account today, then separately ask the CRA, by phone or in writing, to refund the money from the account it wrongly reached. The CRA can grant or refuse that, and it takes weeks. Where paying twice would strain the business, phone the business enquiries line (1-800-959-5525) first and ask them to move the money.

Moving a payment yourself is free. The CRA’s corporate instalment-transfer policy stops transfers once it has assessed the corporation’s income tax return (the T2) for that year, so reconcile those payments before filing. We’d usually recommend reconciling each account against your bank record once a quarter, and monthly if you remit payroll monthly.

What a statement of account shows, and how to get one

The CRA offers a customized statement of account on request, so you can obtain one when reconciling your corporation’s payments.⁴ In My Business Account you can read the balance and transactions at any time under “View and pay account balance”, or order a statement covering any date range through the “Enquiries” service.

A statement lists payments, assessments, later corrections called reassessments, transfers, and each period’s balance, so you can follow how the amount owing changed. Arrears interest, meaning the interest the CRA charges on unpaid tax, keeps compounding daily after the statement is printed. The balance on screen leaves out payments the CRA hasn’t applied yet (e.g. an uncashed cheque), and isn’t an official CRA document.⁵

Your corporation’s separate CRA accounts

Your corporation doesn’t have one CRA account but several. Each has its own fifteen-character program account number (e.g. 123456789 RC 0001): your nine-digit business number, two letters for the type of account, then a four-digit reference number, which is 0001 for your first account of that type and counts up if you open a second.⁶ RC is corporate income tax, RT is GST/HST and RP is payroll, and each carries its own periods, due dates, interest clock and balance. An RC period is a fiscal year, an RT period a GST/HST reporting year, quarter or month, an RP period the month the deductions were withheld.

Money doesn’t move between the accounts merely because you intended a different allocation, so a credit in your GST/HST account does nothing about a payroll debt until you ask for it to be moved. The CRA is under no such restriction, and where your corporation owes money in one account it may take a refund from another and apply it to that debt, telling you afterwards.⁷ While a return the CRA expects is outstanding, though, it releases no refund at all. Filing the missing return is what frees the money.

Where payments go astray

Three entries decide where a payment lands: the fifteen-character account, the period end, and the kind of payment. Period end means the last day of the period the payment settles, entered as a date (e.g. 2026-12-31 for a December year end paying 2026 corporate tax).

Kind of payment does the most damage, because the CRA treats three things as different. An interim payment, also called an instalment, is a part payment of tax made during the year. A payment on filing is the tax due with the return, and a payment against an amount owing settles a balance the CRA already assessed. Your bank’s list is shorter and worded differently, with labels like “Corporation Tax Payments - TXINS” for an instalment and “Corporation Income Tax Balance Due - TXBAL” for a balance.⁸

Timing helps the mistake along. Corporate tax is due two months after the year end, or three for a Canadian-controlled private corporation meeting the small business deduction and prior-year income conditions in our deadline guide. The return isn’t due for six months after that same year end.⁹ Your money therefore sits against a year the CRA hasn’t reviewed, with no filed return to match it against.

Moving a payment back

Two routes run through My Business Account. Open the account holding the misplaced payment and choose “View and pay account balance”. The transfer function there moves money to another period in that account, to a balance owing in it, or to another program account under the same business number, and the corrected balance appears at once.¹⁰ Where that screen won’t do it, the same portal’s “Enquiries” service takes a written transfer request, which buys a record and no hold time against an unpublished wait.

Section 221.2 of the Income Tax Act is what makes either route worth the trouble. A payment moved from one liability to another counts as having been made on the day you originally paid it.³ The arrears interest charged while your money sat in the wrong place gets recalculated on that footing. The provision is discretionary rather than automatic, so check a fresh statement afterwards.

Both routes have limits. Only an authorized officer of the corporation, meaning a director or someone formally authorized on the CRA’s records, can ask to transfer instalment payments, so a bookkeeper with view-only access can’t.¹⁰ The harder boundary is assessment: once the CRA has processed the T2 for the year the payment belongs to and issued the notice of assessment for that year, its published instalment-transfer policy no longer permits that transfer. Fix the allocation before filing, and ask the CRA about other payment errors separately.

Failing that, the business enquiries line (1-800-959-5525) reaches someone who can see the account, at the cost of hold time and no written record. The formal route is a letter to the Corporation Services section of your tax centre, the CRA office that processes your corporation’s returns, which the CRA’s “Find a CRA address” page identifies.¹¹ You can also ask the bank whether a recent payment can still be recalled, though availability and fees depend on the bank.

None of it reaches money paid by somebody else. Section 221.2 only moves amounts between the liabilities of one person, and your corporation, you personally and a second corporation you own are three different people to the CRA. A payment quoting your social insurance number can’t reach the corporation’s account at all.

What the delay costs

The CRA charges interest on overdue corporate tax at its prescribed rate, reset every calendar quarter, and pays a lower rate on a corporate overpayment, both compounded daily.¹² The current quarter’s figures are on our CRA interest rates page, which also prices a balance over a number of days. A misfiled payment therefore costs the full charge on the account that looked unpaid, while the misfiled money itself earns nothing, because refund interest doesn’t run on it.

Refund interest, meaning the interest the CRA pays you when you’ve overpaid, also starts later than you’d think. A corporation with a December 31 2026 year end that filed on time earns none before roughly April 30 2027, however early it paid.¹³

The bigger question is which account the money should have reached. A payroll misallocation is worth fixing promptly, because late remittance can trigger a percentage penalty as well as interest. Late GST/HST payment carries interest; a late return with tax owing can also draw a filing penalty. Late corporate income tax payment alone carries interest.¹⁴

How often this changes

The CRA resets its prescribed interest rates by formula every three months, which is why this guide states no rate and links the page that carries the current quarter’s.¹² The mechanics underneath move far more slowly, and section 221.2, program account numbers and the closing of transfers at assessment are all long-standing. The CRA renames its screens far more often, so treat “View and pay account balance” and “Enquiries” as functions to look for rather than fixed paths. Reconciling is worth a standing calendar entry. Once a quarter, open each CRA account beside your bank statement, tick off every payment your bank shows leaving against one the CRA shows arriving, and chase anything on one side and not the other.

Closing thoughts

The CRA’s own instruction is to review each statement and make sure payments were applied correctly, which puts the checking on you. Two records exist of what your corporation has paid, and they agree only if somebody compares them.

How we handle it

We reconcile a corporation’s CRA program accounts (e.g. corporate income tax, GST/HST and payroll) against the bank record on a cycle rather than only at year end. Where a payment has gone to the wrong period or account, we file the transfer request, then check a fresh statement to confirm the interest came off. Fixing account allocations and chasing payment questions is part of our ongoing CRA support. Formal objections and collections files we take on selectively or refer out.