Pakistani interior secretary Syed Kamal Shah, who returned from a visit to Iran on Sunday, made the complaint to officials in Tehran, media reports said.
Islamabad has made repeated accusations that Indian consulates in Zahidan and cities in Afghanistan are funding tribal militants in Balochistan, including the recently banned Balochistan Liberation Army.
India has countered the allegations saying both Tehran and the international security assistance force in Afghanistan would have known about any such assistance being provided.
The accusations, officials say, are made to discredit India's involvement in various development projects in Afghanistan as well as its close ties with Tehran.
Shah told Iranian authorities that Pakistan was facing problems dealing with militants in Balochistan because of the extreme geographical terrain of the area, the Daily Times reported.
