The routing permits of all airlines flying in the country also will be examined to see if they are violating the rules, said Djoko Murjatmodjo, acting director general of air transportation.
"Who knows if other airlines are also doing the same thing," he said.
The crackdown comes as searchers continue to fight bad weather while combing the Java Sea for bodies and wreckage of the Airbus A320 that crashed Dec. 28, killing all 162 passengers and crew on board.
While the airline is being investigated, Indonesia announced Saturday that it banned all AirAsia flights between Surabaya and Singapore.
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AirAsia Indonesia President Director Sunu Widyatmoko said by text today that the airline will cooperate with the government during the evaluation, but would not comment on the permit allegations until the process is complete.
The ministry also issued a directive Dec. 31 ordering all airlines to provide pilots with up-to-date weather reports before they take off, he said. Currently, it's up to the captain and co-pilot to research and evaluate flying conditions before departing. In other countries, carriers' flight operations departments perform that task for them.
He also planned to meet Monday with the Corruption Eradication Commission to discuss whether to launch a graft probe into AirAsia's operations. Business in the country is commonly conducted using bribery, with payoffs often seen as the most efficient way to get things done.