- Adam Air
- Kartika Airlines
- Trans Wisata Air
Fifteen companies, including six scheduled passenger airlines, were placed in the lowest category and were considered to have met only minimal standards of safety.
The National carrier, Garuda Indonesia, made the second grade.
The six airlines facing a three month deadline are Adam Air, Kartika Airlines, Jatayu, Batavia, Trans Wisata Air and Dirgantara.
The audit was ordered by the government to evaluate transport safety following a string of deadly air accidents in recent months.
Aside from the Adam Air crash off Sulawesi, another of the airline's jets was badly damaged in a hard landing at Surabaya airport in February, although none of the passengers suffered serious injury.
Earlier this month, a Garuda aircraft overshot the runway at Yogyakarta airport and burst into flames, killing 21 people.
Air travel in Indonesia, which is made up of more than 17,000 islands, has grown massively since the liberalisation of the airline industry in 1999 which triggered price wars covering domestic routes.
The rapid growth and price-cutting raised questions over whether safety was being compromised, and if aviation infrastructure and personnel could cope with the huge increase.
Indonesia is also grappling with problems in other modes of transportation.
There have been two serious ferry disasters in recent months killing hundreds of people, while rail accidents on an ageing system built during the Dutch colonial era occur frequently.