Senior Justice Department officials did not move to stop him from sending the letter, officials said, but they did everything short of it, pointing to policies against talking about current criminal investigations or being seen as meddling in elections.

That Mr. Comey moved ahead despite those protestations underscores the unusual nature of Friday’s revelations, which added a dramatic twist to the final days of a presidential campaign. His action also reignited a firestorm that Mrs. Clinton believed she had put behind her when the F.B.I. decided in July not to charge anyone in the investigation into the handling of classified information on her private email server. Mr. Comey’s letter did not reopen that inquiry.

Senior Justice Department officials, career prosecutors and even some in the F.B.I. were at a loss Saturday as to what would happen next. Would Mr. Comey provide a blow-by-blow accounting of the F.B.I.’s steps until Election Day? Did he plan further announcements? Or did he intend, after shaking up the election with his letter, to remain silent about the facts until the presidential votes had been tallied? The F.B.I. offered no comment, and Justice Department officials said they had no idea what Mr. Comey saw as his next move.

Justice Department officials were particularly puzzled about why Mr. Comey had alerted Congress — and by extension, the public — before agents even began reading the newly discovered emails to determine whether they contained classified information or added new facts to the case.