Mario Steven Ambarita breached the fence at the Sultan Syarif Kasim II airport in Pekanbaru city on Sumatra island and survived a one-hour Garuda Indonesia flight to Jakarta by hiding in the aircraft's wheel well on Tuesday.
"The incident serves as a lesson for us," said Julius Barata, a spokesman for the Transport Ministry. "We will strengthen monitoring of airport perimetres so that such incidents will not happen again."
Legislators and security experts said stowaways posed security threats, especially if they involved people with malicious intent.
"Action should be taken against the airport's authority for the negligence," said a legislator, Fary Djemi Francis. "We are very concerned because this incident happened at a time when we are trying to improve aviation safety and national security," he said.
Barata said Ambarita had been flown back to Pekanbaru, where he will be questioned by police and face charges punishable up to a year in prison. He said the man told officials that he wanted to meet President Joko Widodo and ask him why he was not picked as a minister in his cabinet.
"We don't know if he's mentally sound," Barata said. "But he seems to be a smart person because he said he conducted research on the internet and planned the act in advance."
Ambarita climbed into the aircraft's wheel bay as it stopped at the end of the runway before take-off. He came out of the compartment dazed and staggering after the plane landed at the Soekarno-Hatta airport, with blood coming out of an ear, officials said. He was declared healthy after being treated at the airport's clinic. Temperatures can drop to well below zero degrees Celsius outside a plane at above 16,000 feet (4,875 metres), and wheel bays are not equipped with heating or oxygen. Extreme cold and lack of oxygen has killed other stowaways on longer flights.