A federal judge on Thursday ruled in favor of House Republicans in their lawsuit against the Obama administration over ObamaCare.

In a major ruling, Judge Rosemary Collyer, an appointee of President George W. Bush, said the administration does not have the power to spend money on "cost sharing reduction payments" to insurers without an appropriation from Congress.

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Collyer's decision doesn't immediately go into effect, however, so that the administration can appeal it.

At issue are billions of dollars paid to insurance companies participating in ObamaCare so they can reduce customers' out-of-pocket costs, such as deductibles for low-income people.

The House GOP argued that the administration was unconstitutionally spending money on these payments without Congress's approval.

But the administration said it did not need an appropriation from Congress because the funds were already guaranteed by the healthcare reform law in the same section as its better-known tax credits that help people pay for coverage.

Collyer ruled that the section only appropriated funds for tax credits and said the cost sharing reductions require a separate congressional appropriation, which the administration does not currently have.

“Such an appropriation cannot be inferred,” Collyer wrote. “None of Secretaries’ extra-textual arguments — whether based on economics, ‘unintended’ results, or legislative history — is persuasive. The Court will enter judgment in favor of the House of Representatives and enjoin the use of unappropriated monies to fund reimbursements due to insurers under Section 1402.”

Unlike previous ObamaCare lawsuits, this one is not expected to deal a crippling blow to the law if Republicans ultimately prevail.

study from the Urban Institute found that a GOP victory would force insurers to make a major adjustment and hike premiums, but government subsidies would increase to help make up the difference and the system would likely not face major negative consequences.

Still, the case adds a major element of uncertainty to a healthcare system trying to adapt to ObamaCare.

"This is not the first time that we've seen opponents of the Affordable Care Act go through the motions to try to win this political fight in the court system," said White House press secretary Josh Earnest. Earnest said Republicans are trying to "refight a political fight that they keep losing. They've been losing this fight for six years, and they'll lose it again."

He added the lawsuit is unprecedented in terms of its effect on the constitutional separation of powers.

"This suit represents the first time in our nation's history that Congress has been permitted to sue the executive branch over a disagreement about how to interpret a statute," he said.

The challenge arose out of a broader focus on Republicans’ objections to President Obama’s use of executive power in 2014 and amid talk of impeaching the president.

Many experts doubted it would go forward, given that it could be dismissed if a judge decided the House had no legal standing to sue.

But Collyer ruled that the House was directly affected by the administration’s actions and could proceed.

The standing issue could still come up in a higher court when the case is appealed.

Jordan Fabian contributed.

Updated at 2:56 p.m.