In Singapore, Pollycarpus Priyanto, a Garuda pilot at the time and the prime suspect in Munir's trial, left the flight and then went back to Indonesia.

The cabin crew informed the pilot in command that a passenger was sick, and a doctor who happened to be on the plane was asked to provide medical assistance.

[6] When the results of the autopsy were released two months later, on 12 November, the Netherlands Forensic Institute revealed that Munir's body contained a level of arsenic almost three times the lethal dose.

It is alleged that Pollycarpus placed the arsenic in Munir's orange juice, upon orders from Garuda's chief executive at that time, Indra Setiawan.

Indonesian president Susilo Bambang Yudhoyono proclaimed that he will make sure that Munir's killers are brought to justice and quickly convened an independent investigation.

[5][7] In December 2005, Pollycarpus Budihari Priyanto was found guilty of Munir's murder by an Indonesian court and sentenced to fourteen years imprisonment.

[8] In October 2007, Indra Setiawan and his deputy, Rohainil Aini, faced trial for providing Pollycarpus with fake documents to board Munir's flight from Jakarta to Singapore.

[10] In 2007, a Jakarta court found that Garuda was negligent in refusing to perform an emergency landing, and ordered the company to pay 600 million rupiah in compensation to Munir's widow.

[5] In 2014, Hendropriyono admitted to journalist Allan Nairn that he bore "command responsibility" for the assassination, and he was ready to accept being put on trial.

[16] Munir was posthumously awarded the Train Foundation's Civil Courage Prize, which recognizes "extraordinary heroes of conscience".