Jakarta has vowed to investigate allegations Australian authorities paid thousands of dollars for a boat carrying 65 asylum seekers to return to Indonesia, as police say an Australian official has questioned the migrants.

The migrants from Bangladesh, Myanmar and Sri Lanka came ashore on Rote island in eastern Indonesia in late May, after they were intercepted en route to New Zealand by the Australian navy.

The captain and five boat crew, who are all being detained in Rote on people-smuggling charges, told police they were each paid $US5,000 ($A6,470) by an Australian immigration official to turn back to Indonesia.

Indonesia's foreign ministry spokesman Arrmanatha Nasir said the government had received the same information during their preliminary investigations.

"We will investigate further," he told reporters.

"But if that is true, we would truly regret that something like this could happen."

The Australian government has refused to comment on the allegations.

The migrants, including women and children who are being housed in a small hotel in the eastern Indonesian city of Kupang, have corroborated the account given by the crew.

Local police chief Hidayat, who like many Indonesians goes by one name, said an Australian police officer and a New Zealand police officer spoke with the boat people in Kupang on Wednesday, and planned to interview the captain and crew on the island of Rote.

They are later expected to travel to the point where the migrants were intercepted to determine whether it was in Australian or international waters, he added.

The Australian embassy in Jakarta refused to comment.

Australia's conservative government introduced tough immigration policies in 2013 to stop an influx of would-be refugees.

Asylum-seekers arriving on vessels are sent to Pacific camps and vessels are turned back when it is safe to do so, or taken back to their country of origin.