Amnesty International has accused Australian border protection officials of illegally paying people smugglers and endangering lives in a bid to prevent boats of asylum seekers reaching the country.

The human rights group has taken out full page adverts in newspapers in Sydney and Melbourne following the release of a report condemning the government's secretive Operation Sovereign Borders.

This involves a flotilla that has all but stopped asylum seeker boats from reaching the country.

As the migration crisis has unfolded, thousands of asylum seekers from Africa, the Middle East and Central and South Asia have flown to Indonesia to board fishing boats bound for Australia.

Australia's government has rejected Amnesty's report and denied any wrongdoing.

Foreign Minister Julie Bishop said: "Our Australian officials operate in accordance with domestic Australian law and in accordance with our international obligations."

The group claims officials were "complicit in a transnational crime" when they paid people smugglers $32,000 to take a boat with 65 asylum seekers heading for New Zealand to an Indonesian port in May.

Anna Shea, refugee researcher at Amnesty, said: "All of the available evidence points to Australian officials having committed a transnational crime by, in effect, directing a people-smuggling operation, paying a boat crew and then instructing them on exactly what to do and where to land in Indonesia.

"People-smuggling is a crime usually associated with private individuals, not governments - but here we have strong evidence that Australian officials are not just involved, but directing operations."

Fairfax Media reported in June that an Indonesian police investigation had concluded smugglers had been paid more than $30,000 to take a boat full of asylum seekers back to Indonesia.

Ministers at the time denied the Australian Border Force and defence officials had ever paid people smugglers.

However, this denial did not extend to intelligence officials, who are understood to pay criminal informants for information. The government says it does not comment on intelligence or security matters.

Amnesty has also accused Australia of endangering asylum seekers by forcing them from a well-equipped boat onto overcrowded vessels with inadequate fuel for their trip back to Indonesia on two occasions.

Australian officials beat asylum seekers when their boats were turned back, Amnesty also claimed.