WASHINGTON—A federal judge expressed doubt Thursday over efforts by former Trump campaign manager Paul Manafort to have criminal charges against him dropped, but she appeared more receptive to his request to dismiss one of the counts.

At a sometimes testy hearing over three hours, U.S. District Judge Amy Berman Jackson questioned lawyers for Mr. Manafort and special counsel Robert Mueller, who has charged Mr. Manafort in Washington and Virginia with failing to report his work for the government of Ukraine between 2006 and...