Indonesia AirAsia, 49 percent owned by Malaysia-based AirAsia, has made little comment, but said it would fully cooperate with investigations.
While the cause of the crash is not known, the national weather bureau has said the seasonal tropical storms common in the area were likely to be a factor. Last week, the authorities questioned whether the pilot had followed proper weather procedures.
On Monday, the transport ministry said officials at the airport operator in Surabaya and air traffic control agency who had allowed the flight to take off had been moved to other duties while the accident investigation is completed.
It also said it had issued a directive making it mandatory for pilots to be briefed face-to-face by an airline flight operations officer on weather conditions and other operational issues before every flight.
Indonesia is one of the world's fastest growing aviation markets and its carriers, such as Lion Air and Garuda Indonesia , are among the top customers for plane makers Airbus and Boeing.
But its safety record is chequered. The European Commission banned all Indonesia-based airlines from flying to the European Union in 2007 following a series of accidents. Exemptions to that ban have since been granted to some carriers, including Garuda and AirAsia.