Two groups representing 2,000 Protestant and Catholic military chaplains have refused to perform homosexual marriages because they say it violates their beliefs.
The Pentagon says it will not force chaplains to perform same-sex weddings.
Last week, the Department of Defense announced that chaplains could participate in same-sex ceremonies and would even be allowed to use federal facilities for such exhibitions.
The Chaplain Alliance for Religious Liberty, one of the groups representing the chaplains, said allowing same-sex weddings on military bases ignores a federal law banning gay marriage.
"While the memorandum acknowledges a chaplain's right to not participate in same-sex 'marriage' ceremonies -- a right not given by the Pentagon, but rather given by the Creator and protected by the chaplain's faith group -- the new policy makes it clear that the Pentagon has placed the military in the midst of a deeply controversial issue during a time of ongoing war," the organization said.
"By dishonestly sanctioning the use of federal facilities for 'marriage counterfeits' that federal law and the vast majority of Americans have rejected, the Pentagon has launched a direct assault on the fundamental unit of society -- husband and wife," explained Dr. Ron Crews, executive director of the alliance.
The group wants Congress to declare no federal facility may be used to bypass federal law.