A senior Justice Department official, Emil Bove III, denied to Congress on Wednesday that he had expressed to subordinates an intent to ignore court orders to accomplish President Trump’s rapid deportation goals.

The remarks, before the Senate Judiciary Committee, came during Mr. Bove’s confirmation hearing for an appeals court judgeship in Philadelphia, a lifetime appointment that is one rung below the Supreme Court.

Mr. Bove, a key driver of the Trump administration’s sweeping changes at the Justice Department, was repeatedly questioned about a whistle-blower complaint that portrayed political appointees as willing to mislead judges and defy the courts. The complaint, by a former lawyer in the department’s immigration division, Erez Reuveni, said Mr. Bove had shocked subordinates at a meeting on March 14, when he said they might ignore court orders as the administration sent planes of immigrants to a high-security prison in El Salvador.

The New York Times on Tuesday reported on Mr. Reuveni’s account, in which he described witnessing Justice Department leaders planning “to resist court orders that would impede potentially illegal efforts to deport noncitizens.”

At the outset of the hearing, the committee’s Republican chairman, Senator Charles E. Grassley of Iowa, declared he was skeptical of Mr. Reuveni’s account. Democrats and the news media were merely trying to torpedo Mr. Trump’s pick, added Mr. Grassley, who has championed government whistle-blowers for decades.

Mr. Bove’s nomination has generated significant resistance from current and former Justice Department lawyers, as Mr. Bove has led the administration’s efforts to fire, demote and undermine career law enforcement officials who worked on cases that President Trump dislikes. Those include the Jan. 6, 2021, riot at the Capitol; the federal investigations of Mr. Trump; and other cases involving conservatives.