The three men, referred to as trouble-makers by the state-media reports, were killed during a ground and air raid on their hideout in Khorassan Jonoubi Province.
Among the items discovered at the site were a rocket-propelled grenade launcher, numerous heavy hand-weapons and one battle grenade, the reports said.
Three military helicopters took part in the offensive against the rebels.
The men, one of whom was identified as Baluch Zohi, operated in the towns of Saravan and Iran-Shahr, according to the reports.
In recent months, Iranian authorities have stepped up executions in Irans restive eastern provinces.
