By Carl Hulse

The Republican-led House of Representatives won a significant victory over the Obama administration on Thursday when a Federal District Court judge in Washington ruled that the Department of Health and Human Services did not have the authority to spend billions of dollars on a key element of the new health care law.

Judge Rosemary M. Collyer sided with the House in its challenge to the administration’s funding of a program to help as many as seven million lower-income people pay deductibles, co-payments and other out-of-pocket expenses under the law. Congress never provided explicit authority for the spending, she ruled.

“Such an appropriation cannot be inferred,” the judge said in her opinion. She blocked further spending under the program but said that order would be suspended pending an appeal by the Obama administration. No immediate disruption in the program was anticipated.

The judge had been skeptical of the administration’s defense of the program from the beginning and made an crucial earlier decision to grant the House standing to sue. Courts have historically avoided being caught in the middle of fights between the legislative and executive branches.

The 2014 lawsuit, which became as much about separation of powers as the health care law, was initiated by John A. Boehner, who was the House speaker at the time. He was seeking a way to push back against the White House, given that the conservative call to repeal the law, which has been upheld twice by the Supreme Court, was not achievable.

Mr. Boehner, who had been strongly criticized by Democrats for bringing the case, celebrated Thursday’s ruling.

“In the implementation of the health care law and many other significant matters, the Obama administration has engaged in historic overreach that has exceeded the bounds of the president’s authority and deepened the distrust many Americans feel toward their government,” Mr. Boehner said in a statement. “The president of the United States is not a king or a monarch, with the ability to single-handedly create or change the laws of our country.”

Josh Earnest, the White House press secretary, dismissed the judge’s ruling as another instance when Republicans have sought to overturn the Affordable Care Act through the courts. He said the dispute should be settled by voters, not judges.

“This suit represents the first time in our nation’s history that Congress has been allowed to sue the executive branch over the interpretation of a statute,” Mr. Earnest said. “These are the kinds of political disputes that characterize our democracy.”

He added that the administration was confident in its legal arguments. “They’ve been losing this fight for six years,” Mr. Earnest said of congressional Republicans. “And they’ll lose it again.”

Other backers of the administration also predicted that the ruling would be reversed.

“We look forward to the opportunity to have the U.S. Court of Appeals for the D.C. Circuit reconsider Judge Collyer’s unprecedented ruling allowing a partisan faction of Congress to use the courts to settle a political dispute over the interpretation of a statute,” said Elizabeth Wydra, the president of the Constitutional Accountability Center, which filed a brief in the case on behalf of Democratic leaders.

The spending at issue was most recently estimated to reach $130 billion over 10 years. Republican staff members at the House Energy and Commerce Committee identified the money and could find no evidence that Congress ever approved it. House Republicans argued that it was a violation of the constitutional power of Congress to approve all spending.

The House lawsuit is not seen as the same kind of mortal threat to the health care law as earlier challenges that reached the Supreme Court. Backers of the program say it could still function if the administration lost, though other sources of funding would have to be found or the program altered.

However, insurance companies could lose subsidies under the program, potentially driving up premiums and rattling the market. The industry took a wait-and-see attitude on Thursday.

“There is a long judicial process ahead before a final decision is made,” said Marilyn Tavenner, the president and chief executive of America’s Health Insurance Plans, an industry association. “Our members’ focus is and will remain on serving consumers — to ensure their coverage is protected and their health care choices are maintained.”

A version of this article appears in print on May 13, 2016, on page A15 of the New York edition with the headline: Judge Backs Challenge on Health Law.