The mortal remains of Vaaga Bijal Chauhan and Ratandas Makwana were brought to Mumbai by a Pakistan International Airlines (PIA) flight, officials said.
A team of four officials of Fisheries Department of the Gujarat Government was sent to Mumbai yesterday to take possession of the bodies.
The arrangement was made after the Gujarat Government received a message from Indian High Commissioner's office in Islamabad on Tuesday, said Mohammed A Narmavala, Commissioner (Fisheries).
"We spent about three hours at the airport completing the required formalities and left Mumbai at 14:30 pm," he said, adding two ambulances carrying the coffins are on their way to Gujarat.
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Chauhan was a resident of Dandi village, while Makwana hailed from Nanavada village, both in Gir Somnath district.
The bodies will be handed over to the families of Chauhan and Makwana tomorrow for performing the last rites, Rathod said.
The exact cause of their death is not known, but their families suspect they died due to ill-treatment in jail.