Jakarta – The Indonesian military said its troops shot dead on Friday at least 13 men believed to be separatist rebels in troubled Aceh province, where thousands have died in more than two decades of fighting.

The bloody clashes between security forces and guerrillas from the Free Aceh Movement (GAM), which also killed one soldier, occurred two weeks before Jakarta is expected to unveil its new policy for the area.

"The shooting started at 6am during an ambush operation in Bireun. The commander of the operation was shot after he gave warnings to the GAM men ... and nine of them were killed," Zainal Mutaqin, a military spokesman in Aceh, told Reuters by phone.

He added that government troops gunned down four other rebels later in the day near the provincial capital of Banda Aceh, some 1,700 km northwest of Jakarta.

"A squad of 44 soldiers raided a GAM hideout and shot dead four separatists but one of them managed to get away," he said. GAM could not be immediately contacted to confirm the reports.