The Supreme Court on Wednesday declined to overturn a doctrine under which courts defer to federal agencies to interpret their own regulations that come across as ambiguous.

In a 9-0 ruling, the justices narrowed their interpretation of the doctrine, but allowed it to remain in place. The practice means that courts will typically turn to agencies to define exactly what a rule means, if it's not immediately clear, in cases challenging those rules.

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But the justices made clear that the doctrine should only be applied when it's specifically called for, and that courts should be wary of using it too frequently.

"When it applies, [the doctrine] gives an agency significant leeway to say what its own rules mean," Justice Elena Kagan Elena KaganREAD: Supreme Court justices mourn death of Ginsburg, 'an American hero' Democrats, advocates seethe over Florida voting rights ruling Supreme Court denies push to add Green Party candidates to Montana ballot MORE wrote in the court's opinion. "In so doing, the doctrine enables the agency to fill out the regulatory scheme Congress has placed under its supervision."

However, the justices ruled that the case should be sent down to a lower court for reconsideration.

In the case, Vietnam War veteran James Kisor had challenged a Department of Veteran Affairs (VA) rule. He had initially been denied disability benefits in 1982 after saying he developed post-traumatic stress disorder, but was found to be eligible for benefits in 2008.

But the VA issued the benefits under a rule that meant Kisor would only receive them from the time of his new application to reopen his case, filed in 2006, and not apply the benefits retroactively to his initial 1982 request.

Kagan wrote in her opinion – joined by Justices Ruth Bader Ginsburg Ruth Bader GinsburgTrump 'no longer angry' at Romney because of Supreme Court stance Fox News poll: Biden ahead of Trump in Nevada, Pennsylvania and Ohio On The Money: Anxious Democrats push for vote on COVID-19 aid | Pelosi, Mnuchin ready to restart talks | Weekly jobless claims increase | Senate treads close to shutdown deadline MORE, Stephen BreyerStephen BreyerREAD: Supreme Court justices mourn death of Ginsburg, 'an American hero' Ginsburg death sets up battle over future of court Trump's Supreme Court list reveals influence of Clarence Thomas MORE and Sonia Sotomayor Sonia SotomayorToomey, swing state Republican, supports Senate moving on Trump Supreme Court nominee Names to watch as Trump picks Ginsburg replacement on Supreme Court READ: Supreme Court justices mourn death of Ginsburg, 'an American hero' MORE – that courts should not defer to the agency's interpretation "unless the regulation is genuinely ambiguous."

"If uncertainty does not exist, there is no plausible reason for deference. The regulation then just means what it means – and the court must give it effect, as the court would any law," she wrote.

And she said that agencies' reading of the regulation must be "reasonable," that courts can only use an official agency interpretation of a rule, that the interpretation "must in some way implicate [the agency's] substantive expertise" and that the agency definition must also "reflect 'fair and considered judgement.'"

Kagan also pushed back against Kisor's claim that the doctrine means that agencies are intentionally setting vague rules in order to clarify them to their advantage at a later date, saying that "no real evidence—indeed, scarcely an anecdote—backs up the assertion."

She said that Kisor was asking the court to overrule a “long line of precedents" and that doing so "introduces so much instability into so many areas of law, all in one blow." Kagan also said agencies "should have leeway to say what that term means."

While Justice Neil Gorsuch Neil GorsuchAbortion stirs GOP tensions in Supreme Court fight Poll: 59 percent think president elected in November should name next Supreme Court justice The Hill's Morning Report - Sponsored by Facebook - Trump, GOP allies prepare for SCOTUS nomination this week MORE agreed that the court should send the case back down for reconsideration, he vehemently disagreed that the doctrine should remain in place.

"Today’s decision is more a stay of execution than a pardon," he wrote in a concurring opinion that Justices Clarence Thomas Clarence ThomasGOP senator attacks Biden: 'I'm not sure what he recalls' Abortion, gun rights, ObamaCare at stake with Supreme Court pick Rush Limbaugh encourages Senate to skip hearings for Trump's SCOTUS nominee MORE, Brett Kavanaugh Brett Michael KavanaughTrump faces tricky choice on Supreme Court pick The Hill's 12:30 Report: Trump stokes fears over November election outcome The Hill's Morning Report - Sponsored by Facebook - Trump previews SCOTUS nominee as 'totally brilliant' MORE and Samuel Alito Samuel AlitoAbortion, gun rights, ObamaCare at stake with Supreme Court pick READ: Supreme Court justices mourn death of Ginsburg, 'an American hero' Ginsburg death sets up battle over future of court MORE each at least partially joined.

"So the doctrine emerges maimed and enfeebled — in truth, zombified," Gorsuch wrote.

He argued that allowing the doctrine to remain in this form "threatens to force litigants and lower courts to jump through needless and perplexing new hoops and in the process deny the people the independent judicial decisions they deserve."

Gorsuch also criticized the justices for invoking the standard that longstanding precedents should not be overturned unless there's a compelling reason to do so, in their argument that the doctrine should be upheld.

"The court’s failure to be done with Auer, and its decision to adorn Auer with so many new and ambiguous limitations, all but guarantees we will have to pass this way again," Gorsuch wrote, referring to the deference doctrine. "When that day comes, I hope this court will find the nerve it lacks today and inter Auer at last.

"Until then, I hope that our judicial colleagues on other courts will take courage from today’s ruling and realize that it has transformed Auer into a paper tiger."

In a separate opinion, Chief Justice John Roberts wrote that he largely agreed with Kagan's opinion, but sought to argue that the differences between Kagan and Gorsuch's opinions are "not as great as it may initially appear."

And Justice Brett Kavanaugh wrote in a separate opinion that he also believes the doctrine should be overturned, but that he agreed with Roberts that both Kagan and Gorsuch's opinions are not very different.

"In short, after today's decision, a judge should engage in appropriately rigorous scrutiny of an agency's interpretation of a regulation, and can simultaneously be appropriately deferential to an agency's reasonable policy choices within the discretion allowed by a regulation," Kavanaugh wrote.

Updated: 1:22 p.m.