Sources said that Rigi, who took over as chief of Jundullah, the terrorist outfit after his brother Abdul Malik Rigi's execution by Iran, was arrested by "Pakistani army's intelligence organisation."
The news agency did not say where Rigi was arrested.
The development comes in the wake of Iranian President Mahmoud Ahmadinejad asking President Asif Ali Zardari to "arrest and deliver" terrorists operating from Pakistani soil.
Ahmadinejad made the demand during a phone call to Zardari after a suicide attack in the Iranian city of Chabahar on Dec 15 that placed fresh strains on bilateral ties.
Nearly 40 people were killed in the attack, which was claimed by Jundullah.
Since the Chabahar bombing, several Iranian leaders have criticised Pakistan for its failure to end Jundallah sanctuaries on its territory and to prevent cross-border movements of the group's activists.
Abdul Rauf Rigi took charge of Jundullah after his elder brother Abdul Malik was hanged in Iran.
Abdul Malik was arrested by Iranian intelligence agencies in Feb and executed in Jun after being convicted for various crimes, including armed robbery, bombings and attacks on police and civilians.