The trial is the first time army officers have been held accountable for the violence in East Timor, in which elements of the military and its anti-independence militia proxies killed nearly 1,000 people and destroyed much of the territory.
The five are among 18 senior Indonesian officials and militiamen charged with crimes against humanity for allowing the killings to take place in East Timor.
Prosecutor Darmono told the Central Jakarta District Court how on Sept. 6, 1999, militiamen trained and funded by local military and government officials stormed into Ave Maria Catholic Church in Suai, where about 2,000 refugees were taking shelter.
Using knives and homemade weapons, the militiamen killed 27 people, including three priests and 10 women, the court heard.
“The five defendants did not control troops under their command or did not take action even when they knew … that an attack against pro-independence groups was occurring,” said Darmono, who like many Indonesians only uses one name.
The defendants, who could face the death penalty, did not have to enter pleas. The judge then adjourned the trial until next week for further defense arguments.