Amnesty International says the Australian Government has played a role in a transnational crime by paying people smugglers to return to Indonesia.

Amnesty has released a report detailing evidence of Australian Navy and Border Force officials intercepting a people smuggling boat and handing the crew $US32,000 in cash to turn around.

It has called for a royal commission into the alleged payments.

The report said that in May 2015, a boat carrying more than 60 people and six crew believed to be heading to New Zealand was intercepted.

Amnesty says it has spoken to all of the people on board.

They say the boat was intercepted twice and then taken to Greenhill Island near Darwin.

It is alleged that people on board were encouraged to bathe on a Border Force ship, and “it was at this point, on the original boat, that the crew claim the Australian officials gave them money,” the report said.

“The crew told Amnesty International that two of them received $USD6,000 each, and four received $USD5,000 apiece, making a total of $USD32,000.

“One of the 15 asylum seekers who had remained on board described how he saw the captain meeting with the Australians in the boat’s kitchen and saw the captain put a thick white envelope in his shorts' pocket.”

A second alleged incident happened in late July, after which Amnesty says it interviewed 15 people from Bangladesh, Pakistan and Myanmar.

They reported that their boat was pushed back to Rote Island in Indonesia.

“Australian officials appear to have organised or directed the crew to commit a people-smuggling offence,” Amnesty says, claiming it suggests a breach of international law.

“The $US32,000 constitutes a financial benefit to the crew to procure the illegal entry,” the report said.

“The Australian officials who paid the smugglers and instructed them to land on Rote Island in May 2015 may also have participated as accomplices in the transnational crime of people-smuggling.”

The human rights organisation says the payout policy put lives at risk.

“In the cases documented by Amnesty International, Australia turned back people, at least some of whom were asylum seekers, without any assessment of each person's individual situation, including the risk of serious human rights violations or abuses, either in the country to which they were being returned or in another country to which they might be sent.”

Senior ministers have gone to great lengths to deny the involvement of Border Force and Defence Force officials in any payments to people smugglers.

However, that denial has conspicuously not been extended to intelligence officials.

Immigration Minister Peter Dutton’s spokesperson has described the allegations as “a slur on the men and women of the Australian Border Force (ABF) and Australian Defence Force (ADF)”.