The TV report said police were pursuing a group of "counterrevolutionaries who planned sabotage, ethnical disputes and bombings across the country," clashed with them and killed their leader and 11 others near the town of Iranshahr, about 1,600 kilometers (1,000 miles) southeast of the capital, Tehran, the AP reports.
Police also confiscated a "remarkable" amount of explosive materials, bombs and weaponry at the clash site, the report said.
The report did not provide further details or say which group the suspects belonged to.
But a Sunni Muslim militant group called Jundallah, or God's Brigade, which has been blamed for some past attacks on Iranian troops, is known to be active in the area. Jundallah is also believed by some to have links to al-Qaida.
In February, Iran hanged a member of the group, convicted of a bombing that same month that killed 11 members of the Revolutionary Guards in Zahedan, the provincial capital.
Iran has repeatedly accused the U.S. of backing militants and ethnic opposition groups to destabilize the Iranian government. Tensions between Tehran and Washington are growing over allegations of Iranian involvement in attacks on U.S. troops in Iraq , and over Tehran's controversial nuclear program.
A majority of Iran's population is Shiite Muslim but minority Sunnis live in southeastern Iran, a region long plagued by lawlessness. The area, near Pakistan and Afghanistan, is a key crossing point for narcotics, often seeing clashes between police and drug gangs.