AirAsia didn’t have permission to fly from Surabaya to Singapore on the Sunday morning that Flight 8501 crashed into the Java Sea, Indonesian officials said Saturday.

Shortly after Indonesia’s search and rescue agency said it had detected two large parts of the aircraft on the seabed, transport ministry spokesman J.A. Barata said the airline was only permitted to fly the route on Mondays, Tuesdays, Thursdays and Saturdays.

"So AirAsia has committed a violation of the route that has been given to them," Barata told The Wall Street Journal. He said the company's flights from Surabaya, Indonesia's second largest city, to Singapore had consequently been suspended on Friday.

AirAsia used to have permission to fly the route daily, but the number of slots was cut for the period Oct. 26 to March 28 because the country was nearing its quota for flying people to Singapore, said Indonesia’s acting director general of aviation Djoko Murjatmodjo. He didn’t say if other airlines also had their slots reduced.

Murjatmodjo added that AirAsia had been flying the route on Mondays, Wednesdays, Fridays and Sundays rather than the four days designated by the Transportation Ministry. He said the ministry is investigating why AirAsia was flying the route outside its permitted schedule. The probe will include an investigation of the ministry.

"Frankly speaking, it's a bit late for us to find out about this," he said. "One thing that's certain is the days that they are flying aren't the same as the days they were given. There was no request for changes."

At a news conference in Surabaya on Saturday, AirAsia Indonesia’s chief executive Sunu Widyatmoko said the company would fully cooperate with the government investigation. He said the management of AirAsia won’t comment further until the investigation is complete.

Mr. Barata said the investigation will also cover other airlines.

Click for more from the Wall Street Journal.