Two refugees transferred from Nauru to Cambodia as part of a $55 million deal with Australia have returned home, Immigration Minister Peter Dutton says.

The departure of the Iranian husband and wife leaves one person in the country that was part of the initial group transferred from immigration detention as part of the deal.

A spokesperson for Mr Dutton confirmed their return today, saying "refugees can elect to return to their country of origin at any time, which is what an Iranian couple in Cambodia decided to do recently".

In a statement, the spokesperson said the Government remained committed to the resettlement deal with Cambodia.

"The Government holds firm on our policy that if you arrive by boat then you can either return to your country of origin or be resettled in a third country," the spokesperson said.

The couple were part of the original group of four refugees — three Iranians and an ethnic Rohingya man — who were transferred from Nauru in May 2015.

The Rohingya man returned to Myanmar late last year, with the Cambodian Government reportedly stating at the time that the man asked to go because he was homesick.

A fifth refugee was also transferred to Cambodia late last year.

But Labor's immigration spokesman Richard Marles told the ABC only one transferred refugee remained in Cambodia.

Mr Dutton's office said two remained.

Mr Marles said the plan had become "an expensive joke", which had never been a genuine option for refugees.

"It stands as the symbol for how this Government has completely failed in negotiating any third country resettlement options which are credible," he said.

"One of the problems this Government has experienced is it's turned its back on the world... It must start working with the global community and particularly the UNHCR."

Greens immigration spokesperson Sarah Hanson-Young said the Government had not got an exit plan for offshore immigration detention.

Senator Hanson-Young told the ABC the Cambodia deal was "an expensive flop".

Immigration Department not 'immoral rogue agency'

The news of the couple's departure coincide with a 1,200-word defence of the Department of Immigration and Border Protection from its Secretary Michael Pezzullo.

Mr Pezzullo hit out at misleading commentary and reporting on immigration issues, saying that some comparisons — such as those to Nazi Germany — were "highly offensive, unwarranted and plainly wrong".

"The Department and its uniformed operational arm, the Australian Border Force, does not operate beyond the law, nor is it an immoral 'rogue agency'," he said.

"While policy can be debated, there should be no place for falsehood, rumour and unfounded speculation."

Mr Pezzullo said the department shared the same goal as its critics — "to have no children at all in immigration detention, consistent with the law of the land".