Military spokesman Iskandar Sitompul told Xinhua that some Indonesians were among those on board.
Passenger manifest posted at the airbase where the plane took off showed that at least 37 Indonesian people and several journalists were on board, it said.
Taking off from Indonesian airbase Halim Perdana Kusuma in East Jakarta, the plane lost contact at 14:25 Jakarta time (07:25 GMT) while trying to descend from 10,000 feet to 6,000 feet near a small airport in Bogor on its way back to the airbase, said Ervan.
The plane was on the second flight for about 30 minutes shortly after the first successful flight at 12:00 Jakarta time (0500 GMT), he said.
Ervan added that there was no report of bad weather.
Searching operation by rescuers from National Search and Rescue Office and the military have been conducted, Head of Search and Rescue Agency Sudaryatno said.
However, rescue efforts were suspended Wednesday night due to feasibility problems and would be resumed Thursday morning.