On returning, he will first go to Amritsar followed by Patna and Kolkata to hand over bodies to their families.
Minister of State for External Affairs Vijay Kumar Singh, who has flown to Iraq, saluted the remains at the airport as workers loaded the caskets on the aircraft.
"I am going to Mosul to get mortal remains of 38 Indians; we would not get one man's remains as his case is still pending", Singh told news agency ANI.
V.K. Singh is expected to fly back with the bodies in an Indian Air Force Boeing C17 aircraft that can lift up to 70 tonnes of weight. "We will handover the mortal remains to their families".
A group of Indian labourers, mostly from Punjab, Bihar and Himachal, was taken hostage by ISIS when it overran Iraq's second largest city Mosul in 2014. The remaining 39 were taken to Badoosh and killed, she had said.
Families of some of these victims had met External Affairs Minister Sushma Swaraj here on March 26. "We had been saying that we neither have the evidence of them being alive nor the evidence of them being dead". One Indian managed to escape. After the announcement, the Opposition and relatives of the deceased had criticised Sushma Swaraj for the way she broke the news in the parliament and keeping the families of deceased in dark for four long years.
A special plane carrying the bodies of 38 of 39 Indians, who went missing in Mosul in June 2014 and whom the government recently declared dead, is expected to land in Amritsar on Monday.
V K Singh had visited Iraq three times earlier to locate them.