The Supreme Court ruled Thursday that President Obama overstepped his bounds when he tried to circumvent the Senate and install his nominees to key positions — but the justices left the heart of the executive branch’s recess appointment powers intact.

In a ruling freighted with constitutional implications, the justices said the president must wait for Congress to break for at least 10 days before he can use his recess powers, and said lawmakers on Capitol Hill generally get to decide what constitutes a recess.

The 9-0 decision, written by Justice Stephen G. Breyer, amounts to a court-issued spanking of Mr. Obama, and it returns the playing field between presidents and Congress back to where it was before he tried his 2012 end run.

But it was the way Justice Breyer reached his decision — saying decades of clear practice trump the written words of the Constitution — that may have the broader long-term implications. Justice Antonin Scalia, in a stinging concurring opinion, said the court had opened the door to clever lawyers finding yet more ways to expand the president’s powers beyond what the country’s founders intended.

“The real tragedy of today’s decision is not simply the abolition of the Constitution’s limits on the recess—appointment power and the substitution of a novel frame-work invented by this court. It is the damage done to our separation of powers jurisprudence more generally,” Justice Scalia wrote.

Justices were deciding a case stemming from Mr. Obama’s efforts in 2012 to name three members to the National Labor Relations Board. He was unable to get quick Senate confirmation, so he decided to act alone — even though the Senate was meeting every three days in pro forma sessions specifically to deny him his recess powers.

The key clause of the Constitution reads: “The President shall have Power to fill up all Vacancies that may happen during the Recess of the Senate, by granting Commissions which shall expire at the End of their next Session.”

The problem is that the words “recess” and “session” have several meanings in the Constitution and as used in legislative procedure on Capitol Hill.

Mr. Obama had argued that pro forma sessions, wherein the chamber was almost completely empty, little business was done, and the sessions lasted minutes, if not seconds, shouldn’t count. He said the key test should be whether the Senate was available to do business.

But Republican senators argued, and the justices agreed, that even during a pro forma session, legislation can be passed and messages received, which means it was available to act — it just chose not to.

“When the Senate declares that it is in session and possesses the capacity, under its own rules, to conduct business, it is in session for purposes of the clause,” Justice Breyer wrote.

A lower appeals court had gone even further, finding that the recess powers were only restricted to the end-of-year break, and that both the vacancy and the appointment must happen during that time.

Justice Breyer said the Constitution itself was unclear and that the Supreme Court had never ruled on the question, so it made sense to defer to the general understanding the other two branches had reached over the last century. Thursday’s ruling essentially writes that compromise — that a recess must last 10 days — into constitutional law.

“We have not previously interpreted the clause, and, when doing so for the first time in more than 200 years, we must hesitate to upset the compromises and working arrangements that the elected branches of government themselves have reached,” Justice Breyer wrote.

The White House brushed off the rebuke, with press secretary Josh Earnest saying that while they were “deeply disappointed,” they believe the court left them plenty of room to maneuver on other areas of executive authority.

But Republicans said the court ruling strengthens their hand as the House GOP prepares to file a lawsuit challenging Mr. Obama’s use of executive authority in other areas.

“The administration’s tendency to abide only by the laws it likes represents a disturbing and dangerous threat to the rule of law. That’s true whether we’re talking about recess appointments or Obamacare,” said Senate Minority Leader Mitch McConnell, who led fellow Republicans in joining the suit against Mr. Obama’s recess appointment. “I hope the Obama administration will take away the appropriate lessons. Because the court’s decision today is a clear rebuke of that behavior.”

The immediate effect of Thursday’s ruling is to invalidate hundreds of rulings issued by the NLRB, and Republicans said it could also call into question decisions made by Richard Cordray, head of the Consumer Financial Protection Bureau, who was also granted a recess appointment in January 2012.

More broadly, the ruling tinkers with some of the fundamental checks between Congress and the executive branch, though it falls short of the full-scale rebalance that lower courts — and Justice Scalia — said should happen.

Now Congress and the president will have to work out a new normal for recess appointments, and that could involve the executive testing never-used powers to force Congress to adjourn.

In the near term, the opinion will have little effect, because Senate Majority Leader Harry Reid — possibly anticipating the court’s ruling — last year detonated the “nuclear option.” That was a bold parliamentary move to change Senate rules and reduce the number of votes needed to overcome a filibuster on nominees to just a majority vote rather than the 60 required to end most filibusters.

That means Mr. Obama can get most of his nominees through without having to worry about a GOP filibuster — though it does make the process more tedious.

But if a future president were faced with a Senate held by the opposite party, the justices’ ruling would give those senators exceptional leverage in nominations.

In a statement, Mr. Reid said the court’s ruling justifies his use of the nuclear option.

“Without that reform, and with today’s ruling, a small but vocal minority would have more power than ever to block qualified nominees from getting a simple up-or-down vote on the floor,” he said. “Since the November reform, the Senate has been confirming qualified nominees at a steady pace, and today’s ruling will have no effect on our ability to continue ensuring that qualified nominees receive an up-or-down vote.”

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