WASHINGTON — The F.B.I. director, James B. Comey Jr., defended himself Thursday against an onslaught of Republican criticism for ending the investigation into Hillary Clinton’s emails, but he also provided new details that could prove damaging to her just weeks before she is to be named the Democrats’ presidential nominee.

At a contentious hearing of the House oversight committee, Mr. Comey acknowledged under questioning that a number of key assertions that Mrs. Clinton made for months in defending her email system were contradicted by the F.B.I.’s investigation.

Mr. Comey said that Mrs. Clinton had failed to return “thousands” of work-related emails to the State Department, despite her public insistence to the contrary, and that her lawyers may have destroyed classified material that the F.B.I. was unable to recover. He also described her handling of classified material as secretary of state as “negligent” — a legal term he avoided using when he announced on Tuesday that “no reasonable prosecutor” would bring a case against her.

The F.B.I. director repeatedly suggested that someone in the federal government who had done what Mrs. Clinton and her aides did would probably be subject to administrative sanctions.