Home Affairs secretary Mike Pezzullo has sensationally ordered a police investigation into the leak of a classified ASIO briefing on asylum seekers – and the probe will be asked to consider whether it was the Morrison government that broke the law.

A report in The Australian on Thursday revealed the legislation proposed by independents including Dr Kerryn Phelps to allow for the medical evacuation of asylum seekers was a security risk and would require mothballed detention centres to be reopened to cope with the influx.

The report stated that ASIO had warned in a “classified” document the legislation would see up to 1000 asylum seekers on Manus IsIand and Nauru arrive in Australia “within weeks”.

Immediately following the publication, Home Affairs Minister Peter Dutton discussed the ASIO advice on his regular slot with Sydney radio broadcaster Ray Hadley, accusing Labor leader Bill Shorten of ignoring the ASIO warning.

“Bill Shorten now has advice. He’s had briefings. The agencies have told him this bill will be a disaster and will restart boats,” Mr Dutton said.

However, Mr Dutton was later forced to clarify those remarks, after it emerged that Labor had not been offered a briefing on the material that was leaked to The Australian and Mr Shorten’s office condemned the claim as “lies”.

The AFP told The New Daily on Thursday night that it had received the referral from Mr Pezzullo and would now start a preliminary investigation.

“The Australian Federal Police can confirm it has received a referral on Thursday, February 7, 2019, from the Department of Home Affairs in relation to the alleged unauthorised disclosure of classified information,” a spokesman said.

“This referral will be assessed in accordance with AFP standard protocols. As such, it would not be appropriate to comment further at this stage.”

Former border force chief Roman Quaedvlieg told The New Daily on Thursday the latest leaks were “a disgrace” and underlined the risks of the super department that merged immigration and border protection with national security.

The merger was the brainchild of Mr Pezzullo and Mr Dutton, who was appointed to run the super agency.

“Two of the identified risks of a Home Affairs department when we conceived it was the risk of losing clear separation of powers and the perception of politicisation of the agencies,” Mr Quaedvlieg said.

“Recent operational events involving the constituent agencies have resulted in both of those risks manifesting; at least that perception. Winding back that perception is going to take radical and immediate actions, which in the current political climate are unlikely.”

Earlier, Labor frontbencher Jim Chalmers accused the government of “politicising” ASIO.

“I think it’s really concerning to see on the front page of the papers this morning a classified report from one of our agencies,” Mr Chalmers said.

“I think that Scott Morrison has some questions to answer about the leaking of that material. I think most Australians would agree that we wouldn’t want to see our security agencies politicised in the way that they are being politicised here.”

Mr Shorten has hinted this week the ALP may be wavering in its support for the independents’ legislation amid fears the government will use the impasse to frame the election around asylum seeker policy.

Mr Shorten said he wouldn’t be a “purist” over the legislation, prompting a warning from the independents for Labor to hold its nerve.

Mr Dutton also claimed on the Hadley broadcast that Greens founder Bob Brown and leader Richard Di Natale, who are both doctors and activists for asylum seekers, could secure the release of every asylum seeker left on Manus and Nauru under the Phelps legislation.

“Doctors including Dr Bob Brown and Dr Richard Di Natale, potentially, can provide the advice,” Mr Dutton said.

However, Dr Brown later clarified that he was not a registered doctor and this claim was also untrue.