Fazlollah Shahabzi, public prosecutor in the town of Khash, was slightly wounded in the attack on Saturday, the agency said, adding that the "terrorists" escaped after the shooting.
Sistan-Baluchestan, which lies in southeastern Iran, has seen a spate of attacks by Sunni Muslim militant group Jundullah (Soldiers of God) in recent years.
The province is home to a large ethnic Baluch community, who, unlike most Iranians, are Sunnis. The restive area borders Afghanistan and Pakistan and is a major drug trafficking route.
In another incident, gunmen assassinated a Sunni Muslim prayer leader in the northwestern city of Mahabad, the ISNA news agency reported.
"Haj Mamousta Molla Abdolrahim Tina was going home from the mosque after morning prayers and two motorcyclists shot him in the middle of the road," the local public prosecutor, Samad Hazrati, was quoted as saying.
"It has not been clear yet if this was because of political differences or personal issues," Hazrati added.
The report did not specify when the incident happened.
The Kurdish-majority city of Mahabad in West Azerbaijan province has witnessed clashes between police and rebels from the Kurdistan Workers' Party (PKK) over the past two years.
