Two Free Aceh Movement (GAM) agents, one a 17-year-old, were shot and killed during a raid in South Aceh on Friday, military spokesman Ahmad Yani Basuki said on Saturday.
Four rebels were killed in separate incidents in three districts, Basuki said, adding that three others were captured in East Aceh.
Automatic rifles, a satellite phone and a rebel flag were seized, the spokesman said.
However, observers have raised concerns over whether the toll included civilians, pointing out that very few weapons have been captured.
GAM has been fighting for independence since 1976. Over 1100 rebels have been killed since then, while 2000 have been arrested or surrendered.
The Indonesian military has launched an all-out offensive to finish off the GAM and declared martial law in the country on 19 May.