The vessel was heading to Christmas island of Australia with some 250 illegal migrants on board. It sank near the Prigi beach Dec 18. Six other Pakistanis were among some 40 people who survived.
About 90 bodies, including that of the Pakistanis, were fished out of the water, while a search was on for the missing.
Illegal immigrants from Afghanistan, Turkey and the Middle East were also on the boat.
Islamabad was in touch with the Indonesian authorities to bring home the bodies, Xinhua quoted the ministry as saying.
The Pakistani victims belonged to Balochistan province.
Indonesia is a major transit point for illegal immigrants from the Middle East heading to Australia.