On Friday morning, a Justice Department spokeswoman said: “A single district judge should not go beyond the parties before the court in an attempt to block executive branch actions. The Department of Justice’s position is supported by long-standing Supreme Court precedent and should be upheld.”

The spokeswoman, Kelly Laco, did not immediately say whether the administration would appeal.

Bob Ferguson, Washington’s attorney general, who had filed the case along with the National Family Planning & Reproductive Health Association, said his office would return to court to ask the judge to make the injunction permanent.

“He concurred with all of our legal arguments and he rejected all of the administration’s arguments,” said Mr. Ferguson said. “The judge stated from the bench that we met our very high burden to have a national injunction granted.”

The rule, announced in February, would deny clinics across the country millions of dollars from the federal family planning program called Title X. Title X provides $286 million for programs that provide services like birth control, screening for breast cancer and cervical cancer, and screening and treatment for sexually transmitted diseases. These programs serve about four million patients each year, many of them poor, at more than 4,000 clinics.

The rule was partly seen as an attack on Planned Parenthood, which operates about 40 percent of those clinics, is the only provider in some communities, and receives nearly $60 million in Title X funding each year.