Colonel Stephen Henley was tapped to replace Colonel Ralph Kohlmann, who will retire in April, the official said, speaking on condition of anonymity.
Kohlmann, who is the chief judge of the military commissions at Guantanamo, stepped down because he realized that the September 11 trial would not be completed by the time he retired, the official said.
"So he appointed Judge Steve Henley to take over the 9/11 case," the official said.
The American Civil Liberties Union called the timing of the move "highly suspect and disturbing," noting that it came a day after president-elect Barack Obama pledged in an interview with CBS Television to shut down Guantanamo.
"We cannot allow the Bush administration to sabotage president-elect Obama's plans by ramming through these cases in its last days," said Anthony Romero, the ACLU's executive director.