The facility lost about 50% of its connectivity, which is serviced by satellite downlink locations in Maine and Maryland, according to Capt. Robert Durand.
A spokeswoman for Verizon Communications Inc., which maintains and runs the fiber optic line for the military, said service had been restored within 24 hours of the incident.
A military judge is scheduled to hear pretrial arguments Thursday, a day later than originally planned.
Mohammed -- who has been held since 2006 -- is facing charges related to the September 11 attacks.
Meanwhile, the National Transportation Safety Board said its investigation into what caused the train accident was still in the initial stages. Two teenagers sitting on the bridge where the train derailed were killed by coal that spilled from the cars.