A Republican former federal prosecutor, Mr. Comey seemed at first to be laying the groundwork for some kind of legal charge. Speaking sternly, and in far more detail than he usually does, he listed several previously undisclosed findings from the F.B.I.’s investigation:

■ Of 30,000 emails Mrs. Clinton handed over to the State Department, 110 contained information that was classified at the time she sent or received them. Of those, Mr. Comey said, “a very small number” bore markings that identified them as classified. This finding is at odds with Mrs. Clinton’s repeated assertions that none of the emails were classified at the time she sent or received them. The F.B.I. did not disclose the topics of the classified emails, but a number of the 110 are believed to have involved drone strikes.

■ The F.B.I. discovered “several thousand” work-related emails that were not in the original trove of 30,000 turned over by Mrs. Clinton to the State Department. Three of those contained information that agencies have concluded was classified, though Mr. Comey said he did not believe Mrs. Clinton deliberately deleted or withheld them from investigators.

■ In saying that it was “possible” that hostile foreign governments had gained access to Mrs. Clinton’s personal account, Mr. Comey noted that she used her mobile device extensively while traveling outside the United States, including trips “in the territory of sophisticated adversaries.”

■ Mrs. Clinton used multiple private servers for her personal and government business, not just a single server at her home in New York that has been the focus of media reporting for more than a year. Her use of these servers — some of which were taken out of service and stored — made the F.B.I.’s job enormously complicated as it struggled to put together, in Mr. Comey’s words, a jigsaw puzzle with “millions of email fragments” in it.

Despite all that, Mr. Comey said the F.B.I. did not find that Mrs. Clinton’s conduct revealed “intentional misconduct or indications of disloyalty to the United States or efforts to obstruct justice.” But a person in her position, he said, “should have known that an unclassified system was no place” for the emails she was sending. And he said it raised troubling questions about how the State Department handled classified information.