WASHINGTON — The Republican-led House of Representatives won a significant victory over the Obama administration Thursday when a US 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 program under 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 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 found.

“Such an appropriation cannot be inferred,’’ the judge wrote in her opinion. She blocked further spending under the program but said that order would be suspended pending an appeal by the Obama administration.

The judge had been skeptical of the administration’s defense of the program from the beginning and made an earlier crucial decision to grant the House standing to sue the administration. Courts have historically avoided getting 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 Boehner, who was House speaker at the time, as a way to push back against the White House on the health care law, given that the conservative call to repeal the law was not achievable and the Supreme Court upheld the law.

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. And 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,’’ 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,’’ Earnest said. “And they’ll lose it again.’’

But Boehner cheered the ruling. “Today’s Obamacare decision is a victory for the American people, and for House Republicans, who have stood firm for the rule of law,’’ Boehner, now out of the House, said on Twitter after the decision was disclosed.

The spending at issue was estimated to reach more than $136 billion over 10 years. The White House has repeatedly expressed confidence that it could prevail on appeal before the US Court of Appeals for the District of Columbia Circuit.

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.