Then there is the matter of Mrs. Clinton’s family foundation. Keeping accusations about the foundation in the news has been a key Republican strategy to weaken Mrs. Clinton, and the F.B.I. office in New York began a preliminary investigation into it over the summer. Some agents there believe strongly that there is evidence to move forward with subpoenas, a move that has been on hold as part of longstanding policy to not do anything that could influence an election — a policy officials say Mr. Comey violated.

After the election, however, authorities will most likely revisit that decision. Senior F.B.I. and Justice Department officials, including Mr. Comey, have characterized the evidence — and the investigation — as weak, according to several law enforcement officials familiar with the case. They see the case as based on little more than information from “Clinton Cash,” a book by Peter Schweizer that asserted that foreign entities gave money to former President Bill Clinton and the Clinton Foundation, and in return received favors from the State Department.

F.B.I. agents, like many law enforcement officers, are often conservative-leaning. And many of today’s agents came up in the bureau during the 1990s, an era of special prosecutors and mutual distrust between the Clinton White House and the F.B.I. Institutionally, though, the F.B.I. prides itself on nonpartisanship. It investigates public corruption in both parties with equal zeal and has rules and traditions that protect against partisan meddling.

Mr. Comey’s move, and the series of news stories that followed about politically charged investigations, have led to accusations that those rules and traditions had been cast aside.

When the F.B.I. last week published 15-year-old documents about, among other things, President Clinton’s pardon of the financier Marc Rich, the redacted records offered little information but renewed discussion of long-ago Clinton-related controversies, F.B.I. officials said the timing was a coincidence; the requests for the documents had been filed months ago. But it seemed to confirm the suspicions among Democrats that the F.B.I. was out to hurt Mrs. Clinton, a suggestion F.B.I. agents bristle at.

Mr. Comey has sought to position himself as a fiercely independent director who is willing to speak his mind on issues of race, policing and encryption, even when his views are not shared at the Justice Department or the White House. The result has been a much higher profile for Mr. Comey than that of his predecessor, Robert Mueller, as well as for his more low-key boss, Attorney General Loretta Lynch.

Many current and former Justice Department officials expressed dismay that Ms. Lynch did not personally call Mr. Comey and order him, on principle, not to disclose the latest investigative steps in the email case so close to the election.