If your partnership has received a late filing notice for 2016 tax year because the return or extension was filed after March 15, but before April 15th, that notice should be protested pursuant to IRS Notice 2017-71.
Notice 2017-71 provides that any act performed for the 2016 taxable year of a partnership, REMIC, or certain other entities will be treated as timely for all purposes under the Tax Code, except with respect to interest, if the act would have been timely if the Surface Transportation Act had not changed the due date for partnership returns.
There was some confusion at the beginning of the year as to when 2016 partnership returns were due. Due to this confusion, the IRS is providing penalty relief IF the return would have been considered filed timely under the rules prior to 2016.
For more information, contact your ShindelRock tax professional.