The Senate on Tuesday confirmed Emil Bove III, a Trump loyalist whose short tenure in the top ranks of the Justice Department prompted whistle-blower complaints and a storm of criticism from agency veterans, to a powerful federal appeals court judgeship.

Mr. Bove had sparked outcries at the department by directing or overseeing the firing of dozens of employees and ordering the dismissal of bribery charges against Mayor Eric Adams of New York. According to one whistle-blower who went public, Mr. Bove also told government lawyers that they might ignore court orders in pursuit of President Trump’s immigration policy goals.

Mr. Bove has denied being anyone’s enforcer or henchman, but his nomination to a lifetime appointment one rung below the Supreme Court provoked an intense battle in the Senate. His approval to the U.S. Court of Appeals for the Third Circuit, which encompasses Pennsylvania, New Jersey and Delaware, came by a tiny margin, 50 to 49, with all Democrats and two Republicans, Senators Lisa Murkowski of Alaska and Susan Collins of Maine, opposing him.

Still, the confirmation of Mr. Bove provided at least a tacit Senate endorsement of the president’s efforts to bend the justice system to his will. Most Republicans shrugged off concerns that Mr. Bove, 44 and a defense lawyer for Mr. Trump in his Manhattan criminal trial last year, had undermined the traditional independence of the Justice Department or aided in Mr. Trump’s standoffs with the courts.

The day before Mr. Bove’s confirmation hearing, Erez Reuveni, a former immigration lawyer at the department, came forward to assert that Mr. Bove had told subordinates he was willing to ignore court orders to fulfill the president’s aggressive deportation promises.

In recent days, two more would-be whistle-blowers signaled they had additional derogatory information about Mr. Bove, according to lawmakers and advocates. One of those individuals suggested that Mr. Bove was untruthful in at least one of his answers about his efforts to dismiss the Adams case, while another has offered information to the Justice Department inspector general that would seem to support some of Mr. Reuveni’s claims.