Australia's statement at the UN Human Rights Council in Geneva called for Myanmar to conduct its own investigation with international help into what the UN says could amount to ethnic cleansing and crimes against humanity in the country's western Rakhine state, home to more than one million Rohingya.

But Yanghee Lee, the United Nations special envoy for Myanmar, called for a UN inquiry, the strongest form of intervention the council could take, citing evidence that Myanmar may be seeking to "expel" all ethnic Rohingya from the country where they have been living for generations.

"I heard allegation after allegation of horrific events like these - slitting of throats, indiscriminate shootings, setting alight houses with people tied up inside and throwing very young people into the fire, as well as gang rapes and other sexual violence," Ms Lee told the 47-member council.

Human rights groups condemned what they called Australia's weak position at the council, describing already established investigations into the violence by Myanmar as a whitewash.

Htin Lynn, Myanmar's representative in Geneva, rejected any form of international inquiry and dismissed claims of crimes against humanity as "unverified, intentional and one sided".

He said his government is seriously "addressing" the allegations.

In its statement Australia referred to the "scale and complexity of the transition" that Myanmar is undergoing and acknowledged "positive steps" taken by its government since taking office in April last year.

The statement said that while Australia is "deeply concerned" by evidence of serious human rights abuses affecting Muslim communities in Rakhine, Canberra "considers a collaborative approach is the best way to help Myanmar address its human rights challenges, and we remain ready to work with Myanmar in this regard".

"We encourage Myanmar to continue its cooperation with relevant international human rights mechanisms," it said.

On February 16, Australian senators passed a Greens motion without division calling on Myanmar to assert the religious and ethnic equality of all of its people, including Rohingya, and urging the Australian government to consider pushing for a UN commission of inquiry into abuses in the Buddhist-majority country.

Scott Ludlam, who proposed the motion, described what was happening to Rohingya as "devastating".

Emily Howie, director of advocacy and research at Australia's Human Rights Law Centre, told Fairfax Media the wording of Australia's statement in Geneva was "hopelessly weak" and "sweeps under the carpet" the country's crimes against humanity, "no doubt reflecting the Australian trade interests."

She said Australia's position is a "real shame and sits uneasily with the serious concern showed by the Senate across all parties, including the government."

Ms Howie said Australia's position also belies how ill-prepared the Turnbull government is to take a seat on the council.

Australia has been campaigning for a two year term, starting in 2018.

"If Australia acts like this when it sits on the council, its action would have real human consequences ??? it would be leaving thousands of victims to continue to suffer crimes against humanity without a good faith attempt to stop it," she said.

Phil Robertson, deputy Asia director at Human Rights Watch, said during the Geneva negotiations Australia was relegated to a corner as countries like the United States, European Union and even Bangladesh called for an international investigation.

"Australia's human rights policy has literally been at sea for so long with refugee boats that Canberra seems to now instinctively adopt the preferred policy of rights violating Asian nations," he said.

Almost 80,000 Rohingya have fled Rakhine for refugee camps at the Bangladesh border since October when Myanmar's military launched a crackdown following attacks on police posts during which nine policemen were killed.

Rohingya are denied basic rights in Rakhine, including citizenship.

The UN Human Rights Council is expected to vote in late March on the human rights situation in Myanmar, which is also called Burma.

A draft resolution being negotiated includes the establishment of a UN inquiry into "gross human rights violations by the military and security forces" in Rakhine after October 9 last year.