Australia has secretly flown a sixth refugee from Nauru to Phnom Penh under Australia's controversial $55 million agreement with the Cambodian government.

The Syrian man who arrived last Sunday is staying in the offices of the International Organisation for Migration, which has received millions of dollars from Australia to care for refugees in Cambodia.

Australia has flown a sixth refugee from Nauru to Phnom Penh. Credit:AP

But only one of the five other refugees who agreed to take a one-way flight from Nauru since the deal was signed two years ago remains in Cambodia.

Rohingya Muslim Mohammed Rashid, 26, told Fairfax Media in March that he felt abandoned and feared he would die in the country which admitted in April it does not have the social programs to support the refugees.