His allegation has come at the time when India and Pakistan moved a step forward to improve ties between two neighbours.
External Affairs Minister Sushma Swaraj arrived in Islamabad on Tuesday to attend the Heart of Asia conference.
"India was a main hurdle in normalisation of Pakistan-Afghanistan relations," said Rehman Malik while addressing a press conference in Quetta.
"Indian leadership and intelligence agencies did not want Pakistan and Afghanistan to resolve bilateral issues through talks," said Malik, reported Dawn online.
He also alleged that Indian intelligence agency, Research and Analysis Wing (RAW), was involved in terrorist activities in Balochistan, the Federally Administered Tribal Areas and Karachi.
Rehman urged Pakistan government to raise the alleged involvement of RAW in terrorist activities in Pakistan.
"Whenever Pakistan makes efforts to open talks with Afghanistan to resolve issues involving the two counties, Indians create hurdles," Malik said.