The migrants were rescued by the Australian navy in Indonesian waters 11 days ago but were refusing to speak to Indonesian immigration officials, insisting they want to be taken to Australia.
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"We sent officials yesterday to process the migrants according to our law... but they have refused to follow our procedures. We couldn't force them," foreign ministry spokesman Teuku Faizasyah said.
"We just cannot force them to come ashore.
We have to be patient with them."
Indonesia agreed to accept the migrants on humanitarian grounds as part of a new "framework agreement" between Canberra and Jakarta designed to stem the flow of boatpeople from Indonesia to Australia.
The Sri Lankans were originally due to be delivered to a port on Java island last week but were diverted to Bintan amid confusion over how to deal with them and where they should be accommodated.
Faizasyah said the Australian customs vessel, the Oceanic Viking, had "asked for an extension of their stay in Indonesian waters"