The Turnbull government has refused to back an international investigation into atrocities against Rohingya Muslims despite a motion passed in the Senate urging Australia to call for a United Nations commission of inquiry.

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.