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Instead, said John Isaacson, director of, presidents now use their powers to do an end run around the Senate.

“Most of the time, it was not because the Senate was out of business, but because the Senate wouldn’t confirm,” Mr. Isaacson said. “The whole business since the Second World War is related to the contentiousness between the different parts of the federal government.”

But Victor K. Williams, an assistant professor at Catholic University School of Law who filed briefs arguing that the court should reject the case as a political question between Congress and the president, called the judges’ ruling “historically wrong.”

He said the Founding Fathers intended the president to be able to fill positions and that it’s part of the president’s duty to see that the laws are executed.

“This panel of the D.C. Circuit has accomplished what Minority Leader Mitch McConnell failed to do. Minority Leader McConnell said that his No. 1 objective was defeating Barack Obama and Barack Obama’s attempt to govern. This D.C. Circuit panel has been successful where McConnell failed. They have really, effectively challenged the president’s ability to govern,” Mr. Williams said.

The White House now faces some decisions, Mr. Williams said.

It can appeal to the Supreme Court, or it can wait for several other recess appointment cases to make their way through the courts. Alternatively, it could ask the whole D.C. circuit to hear the case en banc — though that option is less likely.

The White House isn’t tipping its hand, but press secretary Jay Carney called the ruling “novel and unprecedented.” He said it contradicts 150 years of practice by presidents of both parties.

“We respectfully but strongly disagree with the rulings,” he said.

Noel Francisco, a lawyer at Jones Day who argued the case for the U.S. Chamber of Commerce and for Noel Canning, the bottling company that challenged the NLRB appointments, said the court returned to the Constitution’s intent, which was to make the recess appointment an emergency power for use only when Congress is not available.

“Issues like this — it’s not about protecting the Congress from the president and the president from Congress,” Mr. Francisco said. “The Constitution draws these lines ultimately to limit the government to protect the people.”