The IRS has identified a delay in processing Form 1040 balance due, Form 1040-X amended, and Form 1040-ES estimated tax payment requests submitted via Modernized e-File. The issue has been resolved, and pending payments are being processed. The taxpayer’s account will be credited with the original requested payment date(s). Taxpayers should not re-submit these payments.
If a taxpayer re-submitted any of these payment requests due to the delay in processing they may cancel them by calling 1-888-353-4537. Cancellation requests must be received no later than 11:59 p.m. Eastern time, at least two business days prior to the scheduled payment date.
If the taxpayer is not able to stop the payment, as seems likely, then it appears the payment’s recovery would depend on the nature of the payment. If the payment was for the first 2021 estimated tax payment, that would appear to be “stuck” in the IRS system until the 2021 return is filed. So the only relief would be for the taxpayer to reduce (or eliminate) the second quarter payment, which means they are going to wait until mid-June to be made whole.
If the payment was for a tax return balance (the Form 1040 or 1040-X), then taxpayers will need to wait for the IRS to determine they have extra funds for the year in question and begin the process of repaying those amounts to the affected taxpayers.