It also said that, three days after the crash, it had issued a directive making it mandatory for pilots to be briefed in person by an airline official on weather conditions and other operational issues before every flight.
"A circular has been signed by the transport ministry on December 31, stating that pilots must have a face-to-face briefing with a flight operation officer so the briefing officer will know the pilot is in a healthy condition and so on," said Djoko Murjatmodjo, acting director general of air transportation.
Aviation experts said this was a common practice in the industry, but it was not immediately clear if it has been normal procedure in Indonesia.
The main focus of the search is about 90 nautical miles off the coast of Borneo island, where five large objects believed to be parts of the plane - the largest about 18 meters (59 feet) long - have been located in shallow waters by ships using sonar.
While experts say the shallow sea should make the recovery fairly straightforward in good weather, strong winds and big waves have frustrated the multinational force of ships and divers that has converged at the site.
"The seas haven't been very friendly, but the black boxes have a 30-day life and they will be able to find them," said Peter Marosszeky, a senior aviation research fellow at the University of New South Wales in Sydney. "It's the weather that is causing the delay."
Thirty-seven bodies of the mostly Indonesian passengers and crew have been recovered, including some still strapped in their seats. Many more may be trapped in the body of the aircraft.
Indonesia AirAsia has come under pressure from authorities, who have suspended its Surabaya-Singapore license, saying the carrier only had permission to fly the route on Mondays, Tuesdays, Thursdays and Saturdays. Flight QZ8501 took off on a Sunday.
It was not immediately clear what difference, if any, the day of the week had on the Dec. 28 flight, and Murjatmodjo made clear that the investigations of the route and the crash were separate.
"Please differentiate between the probe into flight licenses and the air crash investigation," he said.
Singapore's civil aviation authority and its Changi Airport Group said AirAsia had the necessary approvals to operate a daily flight between Surabaya and Singapore.
Indonesia AirAsia is 49 percent owned by Malaysia-based budget carrier AirAsia, whose shares fell nearly 5 percent on Monday.
While the license investigation could have serious consequences for the airline's operations, insurance industry experts said insurers were expected to pay claims whether or not the airline was properly licensed to fly on the day.
The crash was the first fatal accident suffered by the AirAsia budget group, whose Indonesian affiliate flies from at least 15 destinations across the archipelago.