In a statement, the IRGC’s Quds Base said its fighters carried out three joint operations at dawn in the cities of Iranshahr, Khash and Saravan.
According to the statement, 13 militants were killed during the clashes and a number of others arrested.
No details were immediately provided on the affiliation of the militants or casualties among Iranian forces.
The southeastern province of Sistan and Baluchestan, which borders Pakistan and Afghanistan, has long been a flashpoint for armed groups and smugglers.
Last week, state television said five police officers were killed in an armed attack in the province.
No group claimed responsibility for the assault, but the Jaish al-Adl (Army of Justice) group has previously claimed attacks on civilian and military targets in the region.
Iran designates Jaish al-Adl as a terror organization.
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