The UN report concluded that the allegations had "substance" and that the Australian government "has violated [the detainees'] right to be free from torture or cruel, inhuman or degrading treatment".
Two government amendments to immigration legislation would also lead to further inhumane treatment, the report says.
"The Migration and Maritime Powers Legislation Amendment ... violates the Convention Against Torture because it allows for the arbitrary detention and refugee determination at sea, without access to lawyers," the report said.
"The Migration Amendment (Character and General Visa Cancellation Bill) violates the [Convention Against Torture] because it tightens control on the issuance of visas on the basis of character and risk assessments."
But Australian Prime Minister said the report would have "more credibility" if the United Nations gave Australia more "credit" for its actions.
"I really think Australians are sick of being lectured to by the United Nations, particularly given that we have stopped the boats, and by stopping the boats, we have ended the deaths at sea," he said at a press conference in the state of Western Australia.
"The most humanitarian, the most decent, the most compassionate thing you can do is stop these boats because hundreds, we think about 1,200 in fact, drowned at sea during the flourishing of the people smuggling trade under the former government.
"The best thing you can do to uphold the universal decencies of mankind, the best thing that you can do to ensure that the best values of our world are realised is to stop the boats and that's exactly what we have done."
He added that conditions at the Manus Island detention centre were "reasonable under all the circumstances".
"Everyone's needs for food, for clothing, for shelter, for safety are being more than met, thanks to the good work of the [Papua New Guinea] government, the Australian government and the people who are running the centre," he said.
Despite Mr Abbott's rejection of the criticism, Australia is a party to the United Nations Convention Against Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment. It ratified the Treaty in 1989 and is legally bound by it.
Last month Mr Abbott dismissed a separate report by the Australian Human Rights Commission, which criticised the inhumane detention of children in the country's immigration system.
That domestic investigation was a "political stitch-up", he said.
There has been a surge of interest in Australia's immigration system in the UK after Nigel Farage, the leader of the UK Independence Party, said his party would bring in an "Australian-style" regime.
"Let's be honest, the only way forward is UKIP's Australian-style points system proposal, and the only way to ensure this is by voting UKIP in May," Mr Farage said in a statement released earlier this month.
- Independent
