The disaster, in which 135 people died, occurred after a match at Kanjuruhan stadium in Malang, East Java in October last year, sparking questions about safety provisions and the use of tear gas, a crowd-control measure banned by soccer's global governing body, FIFA.
A court in Surabaya will hear charges against five people, including three police officials and one security officer, and a match organiser. If found guilty, they face a maximum prison sentence of five years.
The trial is being held via teleconference due to security concerns, said court spokesperson Agung Pranata.
Indonesia's human rights commission, which conducted an investigation into the stampede last November, found police fired 45 rounds of tear gas into the crowd at the end of the match, causing panic that led to the stampede.
Investigators concluded that excessive and indiscriminate use of tear gas was the main trigger behind the deadly crush.
The commission said locked doors, an over-capacity stadium and failure to properly implement safety procedures exacerbated the death toll.
A lawyer for the match organiser from Arema, one of the football clubs involved in the match, said his client denied all charges.
"If there is negligence it should be on the police, who fired the tear gas, not us," said Sudarman, the lawyer.
Lawyers for police and security officers on trial were not immediately available for comment.
After the incident Indonesian President Joko Widodo announced that all football league matches would be suspended, and that Kanjuruhan stadium would be demolished and rebuilt.
League matches have since resumed in the Southeast Asian nation, but without any spectators.
