Per IRS Publication 4164, specifically sections 1.6.2 and 1.6.2.3, Form 990 short period returns (except for short period final returns) are exempt/excluded from the electronic filing requirement under section 6011(e)(3) and the corresponding regulations, due to IRS limitations that currently prevent the returns and attachments from being filed electronically. Please refer to Publication 4164 for details. You may also contact the IRS Tax Exempt and Government Entities Customer Account Services at (877) 829-5500 for more information on how to proceed with filing the return.