The lawsuit, filed in U.S. District Court in Kansas City, Kan., alleges a pattern of practices that discriminate against non-Christians in the military. It was filed Monday to coincide with the 220th anniversary of the signing of the U.S. Constitution.
The lawsuit names Defense Secretary Robert Gates and Maj. Paul Welborne as defendants.
According to the filing, Spec. Jeremy Hall, a soldier assigned to Fort Riley's 97th Military Police Battalion, received permission to distribute fliers around his base in Iraq for a meeting of atheists and non-Christians.
When he tried to convene the meeting, Hall say, Welborne stepped in, threatening to file military charges against Hall and block his reenlistment.
Attempts to reach Welborne through an Army spokesman weren't successful.
Mikey Weinstein, president of the Military Religious Freedom Foundation, which is helping Hall with his lawsuit, said it is the first of many.
"We're going to expose the pernicious practice and pattern of these massive violations of the Constitution," Weinstein said. "That we had to go to this extent is just a heinous disgrace that defies any possible explanation."
Lt. Col. Jonathan Withington, a Defense Department spokesman, said he wasn't aware of the lawsuit but that the military places a "high value" on the right of military personnel to practice their faith.
"It is DoD policy that requests for accommodation of religious practices should be approved by commanders when accommodation will not have an adverse impact on military readiness, unit cohesion, standards or discipline," he said.
The lawsuit says Hall was forced to "submit to a religious test as a qualification to his post as a soldier."
Hall and the foundation are asking the court to block Welborne from establishing "compulsory religious practices" and order Gates to prevent Welborne from interfering with Hall's free-speech rights.
Since its founding in 2005, the foundation has received nearly 6,000 calls from men and women in the military raising concerns about violations of religious freedom, Weinstein said.
Most callers, he said, were Christians concerned about coercion from superior officers trying to push their beliefs.
Weinstein this year threatened to sue over what he and others called anti-Semitic Bible studies posted by the Fort Leavenworth Command Chaplain's Web site. The documents, first posted in 1999, were removed after Weinstein's foundation raised complaints.
Separately, seven Army and Air Force officers, including four generals, face possible punishment for violating ethics rules by helping a Christian group in the production of a fundraising video.
A Pentagon inspector general's report released this month found that the officers were interviewed in uniform and "in official and often identifiable Pentagon locations."
The report found that none of the officers received approval from superiors to participate in video interviews in an official capacity or in uniform. Air Force and Army officials are reviewing that report.