Police described the October 1 pitch invasion as a riot and said two officers were among the dead, but survivors accused the police of using excessive force.
Officers were seen kicking and beating supporters on the pitch before indiscriminately firing tear gas into the stands.
Football's world governing body FIFA outlaws the use of such riot control methods inside stadiums.
Three local police officers have also been charged over the incident and are awaiting verdicts.
The former director of the company that runs Indonesia's premier league has been named as a suspect and remains under police investigation.
The tragedy has forced Indonesian officials to confront failings in various aspects of the domestic game, which has been blighted for years by shaky infrastructure, mismanagement and violence.
Also read: Indonesian Soccer Stadium Deaths Caused by Tear Gas Use: Chief Minister
Indonesia's National Police sacked its local chiefs for both Malang city and the province of East Java after the tragedy.
The government also suspended all competitive football games but league matches resumed last month.