The Defense Department on Friday warned gay troops that if they disclose their sexual orientation now, they could still get in trouble.
In a new memo, the Pentagon's top personnel chief cited a "legally uncertain environment" facing service members during a court battle over the 1993 law known as "don't ask, don't tell."
The Obama administration is appealing a ruling by a federal judge in California on Tuesday that struck down the law, which bans openly gay service members.
The Defense Department has said it will comply with the court order for now — freezing any discharge proceedings and technically ending its decades-long policy of discriminating against gays. But it is uncertain what would happen if the court grants the administration's request for a temporary stay on the ruling.
If the court agrees to the stay, it is presumed the military would reinstate the old policy.
"We note for service members that altering their personal conduct in this legally uncertain environment may have adverse consequences for themselves or others should the court's decision be reversed," wrote Clifford Stanley, the undersecretary of defense for personnel and readiness.
The Defense Department will continue not to ask service members or recruits about their sexual orientation and to "treat all members with dignity and respect," he wrote.
His memo, released publicly on Friday, was addressed to the civilian chiefs of each military service.
Advocates of lifting the ban have been warning gay troops not to disclose their sexual identity because the court's ruling could be overturned. They say that Congress should step in and repeal the law.
Repeal legislation has passed the House but failed to advance in the Senate because Republicans objected on procedural grounds. Senate Majority Leader Harry Reid, D-Nev., says he will try again to pass the measure in the lame-duck session after the November elections.
In the meantime, troops said no one was sure how to interpret the Pentagon's declaration on Thursday that it planned to comply with the court order.
"To me, that's really signaling that this whole thing is over," said one gay Air Force officer, who co-founded an underground support group for gay troops called OutServe and who uses the pseudonym J.D. Smith.
But, Smith added, the uncertainty will keep him from disclosing his identity.
"What do we do right now? It's creating a lot of confusion at the unit level," he said.
President Barack Obama supports repealing the law. But Defense Secretary Robert Gates says he needs time to complete a study, due Dec. 1, on how to change the policy without causing too much disruption.
Among the issues to be decided is whether gay troops would be given separate housing and if their partners would be given the same benefits of other military spouses.