Indonesia's President Susilo Bambang Yudhoyono has cast doubt over future co-operation with Australia in efforts to stop illegal migration and people trafficking.
Mr Yudhoyono said relations with Australia had entered a "difficult phase" amid increasing tensions over Canberra's decision last month to grant 42 Papuans protection visas.
Indonesia has repeatedly asked Australia to send the group back and has vehemently denied allegations that they would be targeted by Indonesia's military.
The president, who calls the decision incorrect, has indicated he will review cooperation aimed at curbing people smugglers who use Indonesia as a stop-off point to Australia's north.
Mr Yudhoyono's comments come just hours after the Papuans arrived in Melbourne to start new lives.
Their spokesman, Herman Wainggai, 32, said he had fled persecution in Papua and hopes for a peaceful solution to his homeland's bid for independence.
He said they fled Papua to Australia because they are under pressure from the military government of Indonesia.