Indonesia has pulled nine small airlines from service as it intensifies safety efforts following a string of crashes.

Transport Department Directorate General for Aviation Budhi Muliawan Suyitno said the government had revoked the licences of four airlines, and suspended a further five from operation until they meet basic safety standards.

Only the national airline Garuda had managed to improve and be elevated to the highest category, fulfilling 84 per cent of aviation standards, he said.

The safety crackdown follows a string of recent aviation tragedies and near-misses, including a Garuda Airlines crash in Yogyakarta in March that left 21 dead, including five Australians.

"We understand that every consumer has every right to have safety and security," Suyitno said. "The Indonesian government, with the airline operators, have a strong commitment to maintain the safety and security of aviation, and also improve the services through a strong effort to abide by the laws and regulations."

The five airlines that had their licences suspended – SMAC, Kura-Kura Aviation, Germania Trisila, Atlas Deltasatya and Survei Udara Penas – have three months to improve their safety.

"The main problem for Indonesia's aviation... is the lack of human resources," Suyitno said. "We have a scarcity of pilots and technicians."