Officials have said that Flight 8501 was not authorized to be airnborne on a Sunday, as it was Dec. 28 when it went down in the Java Sea en route to Singapore from Surabaya, Indonesia. The airline has been barred from flying that route while an investigation takes place.

The acting director-general for air transport, Djoko Murjatmodjo, said all transport ministry and Surabaya airport officials involved in the unauthorized flight schedule would be suspended.

While there are no indications that the alleged schedule violation was connected to the crash, which is believed to have killed all 162 people aboard the flight, Djoko said authorities were conducting an audit of all flight schedules.

In comments that lay bare longstanding concerns about Indonesia’s nascent aviation sector, Djoko raised the possibility that other airlines, too, could be flying without the required agreements or permits.

“AirAsia was clearly in the wrong because their flight schedules did not conform to the agreement,” Djoko said. “We have suspended the route and will try to find out where the problem lies.

“Now we suspect that other airlines are making the same mistakes. If an investigation reveals violations, we will suspend their routes too.”

Since being deregulated in the 1990s, Indonesia’s aviation sector has been dogged by accidents and safety concerns that prompted the European Union to impose a temporary ban on Indonesian airlines entering its airspace.

AirAsia, the Malaysia-based budget carrier whose rapid growth is emblematic of the booming airline sector across Southeast Asia, had a good safety record and had never previously experienced a fatality.

The airline has said it would cooperate with the investigation but has not commented further on the allegation. Indonesian officials say AirAsia was authorized to serve the Surabaya-to-Singapore route four days a week but not on Sundays.

Gerry Soejatman, an Indonesian aviation consultant, said that if a violation is found, AirAsia is not solely to blame because it had flown that route for two months before the crash.

“This lapse puts more questions on our aviation sector than the crash itself,” Soejatman said. “The government should have known about it. Had this accident not happened, the likelihood is the lapse might have continued.”

Meanwhile, recovery crews battling unfriendly waters pulled three more bodies from the Java Sea but again failed to locate the aircraft’s fuselage, which sonar images have indicated is lying 100 feet below the surface.

A total of 37 bodies have been recovered from the water. But search officials are urgently trying to reach the fuselage, particularly the tail, where the “black box” flight recorders are housed.

Investigators say the recorders hold the key to explaining why the Airbus A320-200 jet crashed as the pilot tried to avoid a thunderstorm. Indonesian government meteorologists say weather was a key factor in the incident but have not ruled out other causes.