The soldiers - Chief Private Seprianus, First Private Husni Dwila and First Private Awaluddin – were accused of raping four women over a period of two days in June of this year.
The military court judgment was broadcast on Elshinta radio station, based in the northern Aceh city of Lhokseumawe. The judge said that the soldiers had traumatised their victims and brought disrepute to their Kostrad special forces regiment.
Aceh’s GAM rebels have been seeking the creation of an independent state on the northern tip of Sumatra for more than a decade. Indonesian troops have been accused of human rights abuses ranging from summary executions, rapes, torture and false imprisonment.
Peace negotiations between the national government and the guerrillas stalled in May and were quickly followed by an all-out government assault on the region.
The army says about 481 rebels have been killed since it launched its offensive on 19 May.
Aceh is home to some of Indonesia’s largest natural gas reserves accounting for between 30 per cent and 40 per cent of all the country's oil and natural gas export production.