Hojjatolislam Mehdi Tavakoli was gunned down by two men in the city of Khash.
The official news agency IRNA reported that Tavakoli, who had travelled to Khash from the provincial capital Zahedan, was shot dead while giving a prayers sermon.
The two gunmen made away on motorcycles, the government-owned news agency Fars said.
The report in IRNA accused the United States of backing Tavakolis killers.
Last night terrorists supported by the White House in the city of Khash, in southern Sistan-va-Baluchistan, martyred a cleric, it said, adding that the U.S. was hoping to create an atmosphere of fear and terror in Iran.
In a separate report, IRNA quoted Hojjatolislam Mohammad-Hossein Moussa-Pour, the Interior Ministrys legal and parliamentary director, as saying, The assassination of the Shiite cleric in Khash took place at the hands of mercenaries who were definitely supported by the U.S. spying agencies.
Irans hardline-dominated Majlis, or Parliament, voted on Saturday to designate the U.S. Central Intelligence Agency (CIA) and the U.S. Army as terrorist organisations.
Sistan-va-Baluchistan Province is home to Baluchis, a predominantly Sunni Muslim ethnic minority.
Iran has witnessed escalating unrest since 2006 in areas populated by Baluchis, who complain of discriminatory and repressive policies by the theocratic regime.
