The lawsuit is being filed after a judge ruled inmates at a federal prison must be allowed the right to group prayer.
The U.S. Supreme Court is hearing a case questioning a New York town's practice of praying before each town board meeting.
The ACLU has filed a petition to hold a federal prison in Terre Haute in contempt of court for not allowing Muslim inmates to pray together five times a day.
John Walker Lindh, who is being held in a federal prison in Terre Haute, has won a lawsuit for rights to daily group prayer.
Instead of individual food recipients being asked to pray before receiving aid, they are now asked afterwards if they would like to pray.
Jackson County Community Provisions has been out of compliance with TEFAP regulations because volunteers invite those receiving aid to pray.