By Robert Pear, New York Times

WASHINGTON — A federal appeals court ruling that limits the president’s power to appoint officials to temporarily run federal agencies when high-level government jobs become vacant has prompted growing concerns among Obama administration officials.

The decision “casts a legal cloud over a wide variety of acting government officers,” including about a dozen senior officials at the departments of Justice, Treasury, Defense, and Health and Human Services and at the Environmental Protection Agency, the administration said in a recent legal brief.

At issue is a decision by the U.S. Court of Appeals for the District of Columbia Circuit, which said in August that federal law generally bars a person from serving, on an acting basis, in a job for which that person has been nominated but not confirmed by the Senate. With some limited exceptions, the court said, the Federal Vacancies Reform Act of 1998 (pdf) “prohibits a person from being both the acting officer and the permanent nominee.”

Congress adopted the law because senators perceived that presidents had been using “acting officers” to circumvent the regular Senate confirmation process.

The issue shows the real-world consequences of the current impasse between President Barack Obama and the Republican-controlled Senate. The number of vacancies at federal agencies is growing, and congressional action on nominees has slowed in the final year of the administration.

Rep. Leonard Lance, R-N.J., raised questions last week about whether federal agencies were complying with the law and the court decision. At a budget hearing, he asked Sylvia Mathews Burwell, the secretary of health and human services, how many officials were serving at her department in an acting capacity.

Burwell named two: Mary K. Wakefield, the acting deputy secretary, and Dr. Karen B. DeSalvo, the acting assistant secretary for health. Burwell complained that delays in Senate confirmation were hampering her ability to run a department that spends more than a trillion dollars a year.

Another top health official, Andrew M. Slavitt, has been nominated by Obama to be administrator of the Centers for Medicare and Medicaid Services but has been unable to get a confirmation hearing. He serves nevertheless as acting administrator of the agency, which provides health insurance to one of every three Americans.

“We work with the Department of Justice to make sure we are in compliance,” Burwell said, without providing details of the government’s legal analysis.

In a recent legal brief, the Justice Department said the court decision “threatens to permanently impair an important presidential power,” to make temporary appointments to vacant positions throughout the government. A Justice Department official said Friday that the administration would seek Supreme Court review of the decision.

Morton Rosenberg, who worked at the Congressional Research Service for 35 years and closely followed debate on the 1998 law, said the court decision was “very correct — consistent with the statutory language and the intent of Congress.”

The debate has directly affected the status of one senior official. Eric K. Fanning was nominated to be secretary of the Army in September, and he became acting secretary in November. But members of the Senate Armed Services Committee expressed concerns about his role as acting secretary, in view of the Vacancies Reform Act.

The Defense Department responded to the senators’ worries. “As a show of comity to address these concerns,” said Peter Cook, the Pentagon press secretary, “Fanning has agreed to step out of his acting role to focus on achieving confirmation.”

The complexity of the situation is illustrated by the multiple roles of Beth F. Cobert, a former executive at McKinsey & Co. Obama has nominated her to be director of the federal Office of Personnel Management. She is already running the agency as acting director. And an administration official said she was still also technically a deputy director of the White House Office of Management and Budget, a title she has held since October 2013.

Frank Benenati, a White House spokesman, said Cobert was “acting within the confines of the law,” was eminently qualified for her new job and should be promptly confirmed by the Senate.

Cobert said she and the White House had “great confidence” in her legal status as acting director of the personnel agency while her nomination was pending. This arrangement, she said, is consistent with “decades of bipartisan precedent and longstanding legal guidance from the Department of Justice.”

The inspector general at the Office of Personnel Management shocked the agency this month when he declared that the Vacancies Reform Act prohibited Cobert from serving as acting director after she was nominated on Nov. 10. The inspector general, Patrick E. McFarland, who retired on Feb. 19 after more than 25 years as the agency’s internal watchdog, told Cobert that “any actions taken by you since the date of your nomination are void.”

The court ruling was issued by a panel that consisted of Judge Karen LeCraft Henderson, who was appointed by President George H.W. Bush, and two Obama appointees, Judges Sri Srinivasan and Robert L. Wilkins. The Obama administration unsuccessfully asked the full appeals court to reconsider the ruling in the case, SW General v. National Labor Relations Board (pdf).

Under the Constitution, the president has another means of filling vacancies, by making temporary appointments to high-level government jobs while the Senate is in recess. In recent years, the Senate has tried to block such recess appointments by holding brief pro forma sessions at which no business is conducted. The interval between such sessions is typically just a few days — not enough time to permit a recess appointment, senators say.

The Supreme Court rebuked the president in 2014, ruling unanimously that he had exceeded his constitutional authority by making recess appointments during brief breaks in the Senate’s work.