A report detailing the inhumane treatment of refugees held on Nauru has been rejected by the Department of Immigration and Border Protection.

Amnesty International and Human Rights Watch (HRW) issued the report yesterday, after travelling to and documenting the conditions for asylum seekers and refugees in Australian-funded detention on Nauru over the past few months.

Titled Australia: Appalling abuse, neglect of refugees on Nauru, the joint report details what are now familiar concerns about mental health, access to adequate medical care, attacks from the local Nauruan population, and concerns for the education and health of the 49 children on the island.

But the department denied many of the claims, stating they were not consulted about the report.

In a statement, it said: "We strongly refute many of the allegations in the report."

"The Republic of Nauru is a sovereign nation and Australia does not exert control over Nauru's functions, its law, its judicial system or law enforcement.

"Australia does, however, provide support to the Government of Nauru by funding accommodation and support services for all transferees and refugees, including welfare and health services."

The department also addressed the fact Amnesty International and HRW were forced to send investigators incognito after a number of requests for official visits were rebuffed or ignored.

"We welcome independent scrutiny of regional processing matters, noting that access to the Centre is a matter for the Government of Nauru … information about independent scrutiny organisations is available to transferees," the statement read.

The Amnesty and HRW researchers, who visited the island separately, spoke to more than 80 of the 1,200 people forcibly transferred and detained on Nauru after seeking asylum in Australia.

Most have been recognised as refugees and live in the community, yet Amnesty researcher Anna Neistat told the ABC they suffer.

"What I found on Nauru is what I can only describe as a deliberate, systematic abuse," she said.

"We're not talking about individual cases, we're talking about patterns, and I think it is quite clear — and in fact I don't think the Australian Government tried very hard to hide it — that essentially they are making an example to prevent further arrivals by boat."