They are thought to be being held near the city of Hobyo.
The Al Kausar was one of three vessels to be hijacked after a five-year lull.
On Sunday sailors from the Indian, Pakistani and Chinese navies freed the crew of a Tuvalu-registered vessel which had been boarded by pirates.
The two crew members who were rescued were in a car that the pirates abandoned after they were chased, Mohamed Hashi Arabey, vice president of Galmudug state, told Reuters news agency.
Pirates contacted by Reuters said they would keep the crew to try to secure the release of more than a hundred pirates jailed in India.
Piracy in the waters off Somalia and Yemen peaked in 2011, with more than 200 attacks.
But it has dropped significantly in recent years, in part because of extensive international military patrols as well as support for local fishing communities.
However, the factors that drove many Somali coastal fishermen to become pirates nearly a decade ago are still there, says the BBC's security correspondent Frank Gardner.
Somalia is currently in the grip of a famine. Poverty is widespread with few employment options for young people.
There is also continued local resentment at the poaching of fish stocks off the coast by Asian trawlers.
Somali security forces have rescued an Indian cargo ship seized by pirates earlier this month, but the hijackers took nine of the 11-man crew when they fled ashore.