On Wednesday afternoon, the highest ranking federal prosecutor in Manhattan, Jay Clayton, was blindsided.

He had just learned that officials in Washington had decided to fire Maurene Comey, a veteran prosecutor in his office, without first notifying him, according to three people with knowledge of the interaction. He was not told the reason.

The sudden firing from the Southern District of New York — and Mr. Clayton’s inability to intervene — raised questions about his autonomy as the leader of an office that has long prided itself on its independence from Washington and has led high-profile investigations into public corruption, financial crimes and gang violence.

The episode typified the chaos that has gripped four U.S. attorney’s offices in the New York region since President Trump reclaimed the White House, taking closer control of the Justice Department than any president in the last half-century and rattling the nation’s legal system.

None of the offices in Manhattan, Brooklyn, Albany and Newark has a permanent leader. Instead, Mr. Trump has concentrated power within the Justice Department in Washington and, in two of the offices, has elevated loyalists with little prosecutorial experience, leading to confusion and plummeting morale within the rank and file.

His moves raise the question of what, exactly, a U.S. attorney is empowered to do, beyond serving Mr. Trump’s chosen agenda.