It was spotted around 2.45am – an hour later than the last time it showed up on civilian radar screens.
General Rodzali Daud said that a military radar installation at a base in Pulau Perak, had detected the plane. A separate military source said it was flying low at the time.
Malaysia's military believes the airliner missing for almost four days with 239 people on board flew for more than an hour after vanishing from air traffic control.
The disclosure raises key questions over the search for the plane, which had initially concentrated on the area where it was last plotted by civilian air traffic control.