"We found weaknesses in the regulatory aspects, in the attitudes, quality and number of personnel and in the lack of up-to-date technology due to shortages of funds," said Diran, a spokesman for a national transportation team set up to evaluate safety.
The country's aviation industry needed more inspectors, the latest technology and greater safety awareness among officials at all levels, he said.
The team is scheduled to release its recommendations on how to limit accidents next week.
Indonesia saw its third major aeroplane accident in as many months last week when a Garuda Boeing 737 overshot a runway in Yogjakarta and burst into flames, killing 21 people.
Dozens of airlines emerged after Indonesia deregulated its aviation industry in 2001, making air travel affordable for the first time for many across the sprawling island nation, and luring passengers away from ferries and trains.
But a series of crashes and other incidents has sparked debate over safety issues.
Last month, the fuselage of an Adam Air jetliner cracked down the middle after a hard landing. No one was hurt.
On New Year's Day, a plane plunged into the sea off Sulawesi. One hundred and two people are thought to be dead from that incident.
Indonesia has also had a number of ferry disasters, including one that killed or left missing more than 400 people, as well as train and bus crashes in recent months.