A total of 61 route schedules were flouted by national flag carrier Garuda, Lion Air, Wings Air, Trans Nusa and Susi Air besides the low-cost AirAsia, according to the Indonesian Transport Ministry.
Disciplinary action will also be taken against 11 officers from the Ministry who were directly involved in AirAsia's unscheduled Surabaya-Singapore route.
The development comes after a probe was launched when it emerged that the crashed AirAsia plane carrying 162 people on board was flying on an unauthorised schedule.
"Garuda Indonesia has committed four violations, Lion Air has 35 violations, Wings Air has 18 violations, Trans Nusa has one violation, and Susi Air has 3 violations," Transport Minister Ignasius Jonan said at a press conference.
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"They committed violations of their permits. They don't have the flight permits (for the 61 routes). It's the same violation as AirAsia," he said.
Earlier, the Indonesian authorities said AirAsia had violated the terms of its licence for the Surabaya to Singapore route by flying on a Sunday, the day the Flight QZ8501 plunged into the Java Sea, following which the carrier's permit for the route was frozen until investigations were completed.
There will be a "thorough evaluation" on processes involving flight slots, Channel News Asia reported, quoting Jonan, who also admitted that there are improvements needed on the part of the regulator and operators in the Indonesian aviation industry.