Four air traffic controllers have been suspended for failing to check the approved flight schedule for AirAsia QZ8501.
Indonesia's transport ministry ordered the suspension of officials, including the general manager of AirNav Juanda airport responsible for allowing AirAsia to take off from Surabaya airport on an unauthorised route on Sunday, 28 December.
"Investigations are underway to ascertain how the airline could fly without the ministry's knowledge," said Djoko Murjatmodjo, the acting director general for air transportation.
AirAsia Indonesia is meant to travel from Surabaya to Singapore every Monday, Tuesday, Thursday and Saturday as part of its winter schedule. But in October, the airline continued to fly routes based on its summer schedule on Monday, Wednesday, Friday and Sunday without seeking permission from the ministry.
Wisnu Darjono, Indonesia AirNav's Director for Safety and Standard, said four officers at Surabaya Airport's air traffic control were removed from their positions because they were "directly responsible for failing to check the approved flight schedule".
He added that no discrepancies had been found on other flights out of Surabaya following a review of its operations.
It is believed AirAsia's revised schedule caused greater pressure on the already overcrowded Surabaya to Singapore route, making it more difficult to create space for pilots to manoeuvre to avoid storms.
Flight QZ8501 vanished after the pilot requested from air traffic control to climb to a higher altitude as he was approaching threatening clouds, but controllers refused the request because there were already six aircraft flying above it. By the time AirNav agreed to approve the ascent it had lost contact with the plane.
Aviation analyst Arista Atmadjati is now calling for the ministry to investigate further into speculation over the changes in flight slots.
"During peak season, stricter measures are needed to ensure that all airlines, including low-cost carriers, are operating according to the regulations," he said.
Atmadjati said Indonesia met less than 60% of the requirements needed before its aviation safety level could be raised by the US Federal Aviation Administration (FAA).
The FAA downgraded Indonesia's aviation safety level to category 2 seven years ago because of a poor safety record.
Other irregularities that have been revealed include the pilots of flight QZ8501 had not received the required weather report from the Meteorology, Climatology and Geophysics Agency (BMKG). AirAsia received the BMKG report at 7am on December 28 - the day of the crash - after the plane's departure at 5.35am and the departure time of the flight had been brought forward from 7am to 5am.
Search teams have recovered 37 bodies from the ocean - some of which were still strapped to their seats. In total 162 people lost their lives. The flight's black box recorders have yet to be found.