The commission will also demand "Notices to Produce" documents from the department over alleged abuse of children in immigration facilities, Secretary Michael Pezzullo told a Senate estimates hearing in Canberra on Monday.

"The commission has kindly informed us that they are in the early contemplative stages, and indeed drafting what they call as a notice to produce documents, which they have indicated to us will be sending to us shortly," Mr Pezzullo said in response to questions from Labor senator Kim Carr.

Last week Fairfax Media revealed that the sweeping national inquiry was investigating the department - the first federal agency to be examined by the commission regarding allegations of sexual abuse. The department said it was only aware of the commission being interested in "historical matters".

Immigration Minister Peter Dutton described the article as "rubbish".

"Well, it's a rubbish story," he told 2GB radio. "Unfortunately they haven't accurately reported that. As I'm advised, the royal commission is seeking advice about some instances from decades ago and the department will comply, they'll provide whatever documents are requested and they'll answer the questions."

But Mr Pezzullo said that Immigration officers had since met with the commission.

"There certainly have been discussions with officers of the commission about a prospective draft notice to produce documentation," he said.

As recently as last week [Immigration officers] have been in contact with the commission," Mr Pezzullo said.

Mr Pezzullo said his department would co-operate with the investigation.

He knew about a number of sexual abuse "incidents" that had occurred since late February in both Australian detention centres and in offshore detention centres such as Nauru, the Senate hearing was told.

According to Senate documents, the Department of Immigration and Border Protection has recorded an additional 28 alleged sexual abuse incidents involving children occurred in Immigration detention facilities from February 2014 to February 2015.

A recent Australian Human Rights Commission inquiry also uncovered 44 instances of children being sexually abused between January 2013 and July 2014.

Mr Pezzullo confirmed these figures, saying 12 cases were still ongoing; 20 had been closed or referred to other authorities and seven had been "declassified". The rest of the cases may have been doubled up, he said.

The royal commission – established by former prime minister Julia Gillard in 2012 – has the ability to investigate churches, charities, community organisations and government bodies. It also has the power to recommend criminal charges.

If the commission decides to hold a public hearing, former immigration ministers, Immigration Department officials and front-line staff could be called to give evidence. The hearing would focus on how the department responded to any abuse, as provided in victim statements.

A spokeswoman for the commission said they did not comment on investigations. She also said public hearings are not announced until four weeks before their commencement date.

Do you know more? Email swhyte@fairfaxmedia.com.au

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