WASHINGTON — The dispute over Hillary Clinton’s email practices now threatens to shadow her for the rest of the presidential campaign after the disclosure on Monday that the F.B.I. collected nearly 15,000 new emails in its investigation of her and a federal judge’s order that the State Department accelerate the documents’ release.

As a result, thousands of emails that Mrs. Clinton did not voluntarily turn over to the State Department last year could be released just weeks before the election in November. The order, by Judge James E. Boasberg of Federal District Court, came the same day a conservative watchdog group separately released hundreds of emails from one of Mrs. Clinton’s closest aides, Huma Abedin, which put a new focus on the sometimes awkward ties between the Clinton Foundation and the State Department.

The F.B.I. discovered the roughly 14,900 emails by scouring Mrs. Clinton’s server and the computer archives of government officials with whom she corresponded. In late July, it turned them over to the State Department, which now must set a timetable for their release, according to Judge Boasberg’s order.

While the emails were not in the original trove of 55,000 pages that Mrs. Clinton’s lawyers handed to the State Department last year, the F.B.I. director, James B. Comey, said in July that he did not believe they had been “intentionally deleted.” Still, he characterized Mrs. Clinton’s handling of classified information during her years at the State Department as “extremely careless.”