The Homeland Security department's U-turn, which was published in its latest policy guide, follows a lawsuit filed by three churches damaged by Hurricane Harvey in August 2017.
Harvest Family Church in Cypress, Hi Way Tabernacle in Cleveland and Rockport First Assembly of God all sustained heavy damage from flooding after Hurricane Harvey but were told they are not eligible for FEMA aid.
Under the new policy, "private non-profit houses of worship are now eligible for disaster assistance as community centers, without regard to their secular or religious nature".
Pastor Charles Stoker from Hi-Way Tabernacle told ABC News that his church was "nearly destroyed" by more than 30 inches of floodwater after Hurricane Harvey.
He said FEMA was being "unfair".
The new policy will apply to disasters declared on or after 23rd August 2017 but it is not clear how it will affect the lawsuit, which is currently on appeal.
