The head of the Immigration Department has "categorically refuted" new allegations from Amnesty International that the conditions on Nauru for refugees and asylum seekers "amount to torture".

In the report titled Island of Despair, the international human rights organisation also accused the Federal Government of flouting international law, and running a "deliberate policy to inflict harm on refugees".

The secretary of the Immigration Department, Mike Pezzullo, had not read the report when he was questioned about it in a Senate Estimates hearing on Monday night.

"It doesn't surprise me, Senator, because I've seen Amnesty International reports that say similar things," Mr Pezzullo told the committee.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 13 minutes 7 seconds 13 m Anna Neistat says most refugee children are not attending the local schools because of fear.

"I refute categorically, both on behalf of my own department and by way of explaining government policy in this regard, that it's not the Australian Government's position, nor the position of this department, that we flout any laws, international or otherwise.

"I understand both the legal as well as philosophical definition of torture and that is not a practice that's been engaged upon at all."

Greens Senator Nick McKim clashed repeatedly with Coalition senators as he put a series of quotes from the report to Mr Pezzullo and Government Minister Michaelia Cash.

"I'm speaking on behalf of people who don't have a voice at the moment, and I won't be silenced by you," Senator McKim said.

"The conditions on Nauru — refugees' severe mental anguish, the intentional nature of the system, and the fact that the goal of offshore processing is to intimidate or coerce people to achieve a specific outcome — amounts to torture," he read from the report.

'We must be visiting different islands': Pezzullo

Amnesty International said its findings were based on desk research and field work carried out on Nauru between July and October.

Amnesty's senior research director, Anna Neistat, told Four Corners interviews with 58 refugees and asylum seekers on Nauru revealed high levels of mental health issues, and safety fears which were preventing children from attending school.

But Mr Pezzullo said he had visited Nauru last week.

"There are no restrictions on my access to the facilities and I'll compare the field research that purports to be at the basis of this report with my own observations and that of my officers," he said.

"We might be visiting different islands, and we might be living in alternate, parallel universes."

"I don't think so," Senator McKim responded.

The Immigration Department said it will review the report, and follow up on any new information.