A day after a judge in California ordered the Pentagon to cease enforcement of its policy barring gays from openly serving in the military, Gates told reporters that the question of whether to repeal the law should be decided by Congress, and done only after the Pentagon completes its study on the issue.
"I feel strongly this is an action that needs to be taken by the Congress and that it is an action that requires careful preparation, and a lot of training," said Gates. "It has enormous consequences for our troops."
The defense secretary said that besides the changes in training, regulations will need revisions and changes may be necessary to benefits and Defense Department buildings.
The battle in the courts over gays in the military may be far from over. The Justice Department is considering whether to appeal the court ruling and its first response may well be another trip to the courtroom of U.S. District Judge Virginia Phillips in Riverside, Calif., to seek a stay, or temporary freeze, of her ruling. If Phillips turns down the request, the Justice Department would likely turn to the federal appeals court in California.
It was unclear whether Phillips' injunction against the 17-year-old policy on gays in the military would affect any ongoing cases.
If the government does appeal, that would put the Obama administration in the position of continuing to defend a law it opposes.
Gay rights groups warned gay troops not to disclose their identity for now. Aaron Tax, the legal director for the Servicemembers Legal Defense Network, said he expects the Justice Department to appeal the case to the U.S. 9th Circuit Court of Appeals.
"Service members must proceed safely and should not come out at this time," Tax said in a statement.
Gates, a Republican, and Mullen face disagreement among the most senior general officers on whether lifting the ban would cause serious disruption at a time when troops are fighting in Afghanistan and winding down a long war in Iraq.
For example, the incoming Marine commandant, Gen. Joseph Amos, and his predecessor, Gen. James Conway, both have told Congress that they think most Marines would be uncomfortable with the change and that the current policy works.
In part to resolve the question of how the troops feel, Gates has ordered a study due Dec. 1 that includes a survey of troops and their families.
Mr. Obama agreed to the Pentagon study. Mr. Obama also worked with Democrats to write a bill that would have lifted the ban, pending completion of the Defense Department review and certification from the military that troop morale wouldn't suffer. That legislation passed the House but was blocked in the Senate by Republicans.
Democrats could revive the legislation in Congress' lame-duck session after the midterm election.
Family Research Council President Tony Perkins accused Phillips of "playing politics" with national defense.
"Once again, an activist federal judge is using the military to advance a liberal social agenda, disregarding the views of all four military service chiefs and the constitutional role of Congress," he said.
Perkins urged the Justice Department "to fulfill its obligation to defend the law vigorously through the appeals process."
Gates has said the purpose of his study isn't to determine whether to change the "don't ask, don't tell" law, which is something he says is probably inevitable but for Congress to decide. Instead, the study is intended to determine how to end the policy without causing serious disruption.
Coming just three weeks before voters go to the polls, Tuesday's ruling seemed unlikely to force a final weeks' change of strategy or message as candidates pounded home their plans to help put back to work the 15 million Americans lacking jobs.
Polls suggest the economy is driving voters' choices, pushing national security and social issues down on their list of concerns.