WASHINGTON — In a victory for President Trump’s effort to trim the ranks of the federal bureaucracy, the fired head of a federal watchdog agency says that he will abandon his legal battle against the Trump administration to get his job back. 

The head of the federal Office of Special Counsel, Hampton Dellinger, contends that he likely faced a tough road before the Supreme Court. Mr. Dellinger said he was dropping his case a day after a panel of judges on the United States Court of Appeals for the District of Columbia Circuit sided with the Trump administration in removing him from his post atop an independent agency designed to handle disputes over personnel policy within the federal workforce.

“My fight to stay on the job was not for me, but rather for the ideal that OSC should be as Congress intended: an independent watchdog and a safe, trustworthy place for whistleblowers to report wrongdoing and be protected from retaliation,” Mr. Dellinger said in a statement emailed to the Sun and other news organizations.

Mr. Dellinger’s removal could threaten efforts his office has made in recent days to challenge the Trump administration’s firing of thousands of federal employees. Hours before he was ousted Wednesday, a government personnel board ruled that more 5,000 fired employees should be put back on the job at the Department of Agriculture following a request from Mr. Dellinger’s office.

It was not immediately clear who would replace Mr. Dellinger as special counsel. The case had become a flashpoint in the debate over how much power the president should have to replace the leaders of independent agencies as he moves to radically reshape and shrink the federal government. 

Mr. Dellinger’s lawyers had argued that it’s essential for the special counsel to remain independent from the president in order to properly perform their duties without political interference. Mr. Dellinger sued Mr. Trump last month after he was fired in an email with no explanation, despite a law that says special counsels can be removed by the president “only for inefficiency, neglect of duty, or malfeasance in office.” 

A federal district judge, Amy Berman Jackson, who was nominated to the bench by President Obama, quickly reinstated Mr. Dellinger in the job while he pursued his case. Judge Jackson on Saturday ruled that Mr. Dellinger’s firing was unlawful and ordered that he remain in his post. 

On Wednesday, though, a three-judge panel of the District of Columbia Circuit lifted Judge Jackson’s order blocking his removal, allowing the Trump administration to replace him while the judges weigh the legal arguments.  It had been expected that the case would ultimately be decided by the Supreme Court, which has a majority of conservative justices.

Mr. Dellinger said the appeals court’s decision means the office “will be run by someone totally beholden to the President” for the months before he could get a final ruling before the Supreme Court. Mr. Dellinger added that he believed his “odds of ultimately prevailing before the Supreme Court are long.”

“I think the circuit judges erred badly because their willingness to sign off on my ouster — even if presented as possibly temporary — immediately erases the independence Congress provided for my position, a vital protection that has been accepted as lawful for nearly fifty years,” Mr. Dellinger said.