e-file Waiver Issue: Substituted Return Process


If a taxpayer has a business need to file a subsequent corporate income tax return for the same tax period prior to the extended due date of the return, the taxpayer should request a waiver.  If the waiver is approved, the taxpayer will be required to file the  original return on paper and then the substituted (subsequent) return electronically.

The primary situation in which this will apply is when a corporate taxpayer required to file electronically has a net operating loss it wants to carry back.   To obtain a quick refund of prior period taxes by carrying back a NOL, a taxpayer generally files Form 1139, Corporation Application for Tentative Refund.  The instructions for filing the Form 1139 require that the Form 1120, U.S. Corporation Income Tax Return, be filed no later than the date the taxpayer files the Form 1139.  Since many large taxpayers do not have  final numbers and supporting documents for their Form 1120 in time to file the Form 1139, they file a  tax return supporting the net operating loss realized and also a Form 7004,  Application for Automatic 6-Month Extension of Time To File Certain Business Income Tax, Information, and Other Returns.  The extension allows the taxpayer time to confirm the numbers on its return.  Simultaneously  with its tax return (or soon after), the corporation files the Form 1139 based on the  return.  During the extension period the corporation  generally files a substituted return containing  final information. The last return filed within the extension period replaces any prior filing, so it is substituted for the prior submission.

A taxpayer with this situation and subject to the corporate e-filing mandate will be required to:

  • Request a waiver following the instructions in Notice 2010-13.
  • Identify the waiver on the subject line or in the body as a Substituted Return Waiver.
  • After waiver approval - file the original return on paper.  This return must be a valid return with sufficient data to calculate tax, and must reflect an honest and reasonable attempt to satisfy the requirements of the tax law.  An application for a tentative refund may be disallowed if there are any material omissions or math errors that are not corrected within the 90-day period the IRS uses to process the application.
  • File the substituted return electronically by the due date as extended.