The Defense Department has said it would comply with Phillips' order and had frozen any discharge cases. Pentagon spokeswoman Cynthia Smith said recruiters had been given top-level guidance to accept applicants who say they are gay.
Recruiters also have been told to inform potential recruits that the moratorium on enforcement of the policy could be reversed at any time, if the ruling is appealed or the court grants a stay, she said.
Gay rights groups were continuing to tell service members to avoid revealing that they are gay, fearing they could find themselves in trouble should the law be reinstated.
At least two service members discharged for being gay began the process to re-enlist after the Pentagon's Tuesday announcement.
Phillips said keeping gays from openly serving in the military violates the First Amendment and is bad for military readiness and recruitment.
But the Justice Department and the Obama Administration says repealing the policy could damage troop morale as they fight two wars, which is why the government had asked Phillips to delay her Oct. 12 injunction on the policy. They say the military needs time to prepare new regulations and train and educate service members about the change.
Phillips has said her order does not prohibit the Pentagon from implementing those measures.
Justice Department officials say the Obama administration will appeal to the appellate court in San Francisco. The issue could go all the way to the Supreme Court.
President Barack Obama has said that he wanted to end the military's policy against gays, but he prefers that it be done in Congress. So far, Senate Republicans have blocked the bill from passing.
The Associated Press contributed to this report.