The refugees were denied visas and kept in detention centres for more than two years, the UN report said.
The decision comes amid an Australian election campaign in which rival parties debate how to curb an influx of asylum-seekers.
The government says the refugees were considered potential security threats.
Figures from Australia's Department of Immigration; passenger numbers exclude crew
The UN Human Rights Committee report released on Thursday finds Australia denied the refugees a chance to challenge their detention, amounting to cruel, inhuman and degrading treatment.
The refugees - including 42 Sri Lankan Tamils, three Rohingya Muslims from Myanmar and a Kuwaiti - arrived at Australia's remote Christmas Island between March 2009 and December 2010.
They were denied visas and indefinitely detained after the Australian Security Intelligence Organisation determined they posed specific risks.
The sharp rise in asylum seekers has become an increasingly contentious topic as rival political parties vie to crack down ahead of the September general election.
In July, Labor Party Prime Minister Kevin Rudd announced asylum seekers arriving by boat would no longer be resettled in Australia.
Instead, they would be transported to Papua New Guinea, a decision the UN High Commission for Refugees called "troubling".
The "hard-line decision" was taken to ensure border security and to dissuade people from making the dangerous journey to Australia by boat, Mr Rudd said.
Meanwhile, opposition leader Tony Abbott has pledged his own crackdown, recommending three-year temporary visas and required participation in a work-for-welfare programme without rights to appeal or permanent residency.
Thousands of asylum seekers attempt to reach Australia by boat every year.
A United Nations watchdog group says Australia has treated 46 detained refugees in an "inhuman" way and should release them.