Military chaplains are seeking assurance from Congress and the Pentagon that troops who express religious objections to homosexuality won't suffer reprisals.
In a joint letter, 21 religious agencies that provide chaplains to the military expressed concerns that the repeal of "Don't Ask, Don't Tell" could marginalize or silence troops who believe same-sex relationships are immoral.
"Service members should know that chaplains' ministry and their own rights of conscience remain protected everywhere military necessity has placed them," group leaders said in the letter.
The signatories, who themselves are respected veteran military officers and chaplains, also noted that "endorsers and faith communities had no voice in the formulation of such a significant policy change."
"DOMA remains the law of the land," they said. "There is no clear reason why it does not apply to federal military facilities, particularly base chapels."
"Since the current administration has publicly stated that it will no longer support and defend DOMA, this action has every appearance of selective disregard for the law and raises significant concerns," they concluded.
Meanwhile, military training to prepare service men and women for the implementation of the new law is expected to be complete by the middle of the summer.