The 12 asylum seekers who fled Sri Lanka and reached the Cocos Islands on May 2 were all arrested on arrival at Colombo airport after being deported by Australian authorities on May 5.
The group, which is believed to include children and an infant as young as one, were handed over to Sri Lanka's Criminal Investigation Department.
The immigration department refused to answer questions about the boat's arrival or the fate of its passengers, saying "we do not comment on operational matters".