The UN Subcommittee on Prevention of Torture says it has been obstructed from carrying out its protective mandate, violating Australia's obligations under UN protocols.
The 12-day tour was due to continue until Thursday, but the UN party has left the country early.
"It is deeply regrettable that the limited understanding of the (subcommittee's) mandate and the lack of co-operation stemming from internal disagreements, especially with respect to the states of Queensland and NSW, has compelled us to take this drastic measure," UN delegation head Aisha Shujune Muhammad said in a statement.
NSW prevented access to court cells and prisons while Queensland stopped delegates inspecting mental health wards.
Academics and advocacy groups condemned the states for blocking access.
"States' parties have an obligation to both receive the (subcommittee) in their territory and allow it to exercise its mandate in full, including by allowing unfettered access to places of detention," said a joint statement circulated by Australian Lawyers for Human Rights and signed by dozens of other groups and individuals.
Corrections Minister Geoff Lee told a budget estimates hearing on Monday the NSW government supported the subcommittee's objectives.
Asked whether he was concerned the state's facilities would not satisfy UN inspectors, Dr Lee said there were other issues - regarding funding and security - the state needed to sort out with the federal government.
"We haven't been able to reach a landing point where we are happy with its operational security and until we do that we will continue to not allow the UN inspectors," Dr Lee said.
"I have every confidence in our correctional facilities, they meet and many times often exceed those of other countries."
Senior minister David Elliott, a former corrections minister, said he made sure past premiers did not approve the UN inspections.
"I'm not going to have UN inspectors from Iran and China and Cuba come into NSW jails and tell us that we're doing things wrong," he told 2GB on Monday.
Mr Elliott said the federal government encouraged the inspections, but was protected from having to open immigration detention centres or defence force correctional facilities, unlike state prisons.
Dr Lee also apportioned blame federally.
"The federal government did sign us up, and they said that they would consult and work with us, now we haven't reached that point," Dr Lee said.
Premier Dominic Perrottet defended NSW preventing the UN delegates' entry to prisons last week.
"Our prison system is there ultimately to do one thing and that is keep the people of NSW safe," he said.
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