Australian Federal Police officers have raided the ABC’s offices in Sydney over a series of reports into alleged unlawful killings by Australia’s elite special forces in Afghanistan.

Just 24 hours after a similar raid in Canberra on the home of News Corp journalist Annika Smethurst, police descended on the national broadcaster on Wednesday.

The ABC series, like the News Corp report, relate to secret documents marked “AUSTEO”, which means “for Australian eyes only”.

Two years ago, the ABC reported that “hundreds of secret defence force documents leaked to the ABC give an unprecedented insight into the clandestine operations of Australia’s elite special forces in Afghanistan, including incidents of troops killing unarmed men and children”.

“The documents, many marked AUSTEO — Australian Eyes Only — suggest a growing unease at the highest levels of Defence about the culture of Australia’s special forces as they prosecuted a bloody, secretive war against insurgents across a swathe of southern Afghanistan,” the report states.

“One document from 2014 refers to ingrained ‘problems’ within special forces, an “organisational culture” including a ‘warrior culture’ and a willingness by officers to turn a blind eye to poor behaviour.”

The report was prepared by the investigative journalist Dan Oakes and Sam Clark, who is now the executive producer of Insiders.

#BREAKING 3 AFP officers have just entered the ABC office in Ultimo @10NewsFirstSyd @10NewsFirst pic.twitter.com/jrGDjl5fNh

— Charlotte Goodlet (@cgoodlet) June 5, 2019

ABC managing director David Anderson said the police raid was highly unusual.

“This is a serious development and raises legitimate concerns over the freedom of the press and proper public scrutiny of national security and defence matters,” he said.

“The ABC stands by its journalists, will protect its sources and continue to report without fear or favour on national security and intelligence issues when there is a clear public interest.”

Meanwhile, the Prime Minister’s office confirmed on Wednesday that it was a Department of Defence referral that sparked the seven-hour police raid on Ms Smethurst’s home.

But the government has rejected as “ludicrous” any suggestion that it orchestrated the raid, adding the investigation was aimed at the leaker, not the journalist.

The AFP raid on Ms Smethurt’s home on Tuesday came more than a year after publication of a story quoting top secret correspondence about new spy powers to tackle cybercrime, including child pornography.

Police spent hours combing through Ms Smethurst’s kitchen, even her oven, cookbooks and underwear drawer, in a raid that News Corp has called “heavy handed” and “intimidatory”.

BREAKING Federal police are raiding the ABC’s Ultimo HQ over a series of stories known as The Afghan Files. Search warrants for Dan Oakes, Sam Clark and our news director Gaven Morris #auspol @abcnews @withMEAA pic.twitter.com/P183av5hEB

— Jason Om (@jason_om) June 5, 2019

Attorney-General Christian Porter said he completely rejected the suggestion the raid was a deliberate attempt to intimidate a journalist or that “the timing of it has been structured by the government, or demanded, or required, or orchestrated by the government”.

“That is just utterly untrue. This is an investigation from the AFP, it is done completely independent of executive government,” Mr Porter told the ABC.

“The investigation is, as I understand it, under the very long-standing provision of the Crimes Act that relates to the official misuse of unauthorised or information, so an unauthorised disclosure of the information by an official to a third party. So the investigation, if I can summarise in broad terms, is not about the journalist per se, it’s about someone who may or may not have made an unauthorised disclosure against the terms of a very well-known provision of the Crimes Act to a third party.

“Unauthorised disclosure of information might give rise to both accurate or inaccurate reporting, and particularly in circumstances of inaccurate reporting, that could have conceivably a bearing on national security, just as it could if it were accurate.”

The original story, published in The Sunday Telegraph in April 2018, related to the activities of the Australian Signals Directorate, an intelligence and security agency that collects foreign intelligence and provides advice and assistance on information and cyber security.

AFP RAID: we’ve gone to level 12 where ABC lawyers (and me) meeting the three AFP officers to discuss the warrant which they are executing. Three journalists named on warrant. More to come…

— John Lyons (@TheLyonsDen) June 5, 2019

The original report was condemned as “completely wrong” by Home Affairs Department secretary Mike Pezzullo.

He said it implied agencies were seeking new surveillance powers to spy on Australians’ emails and mobile phones. In fact, he argued the actual proposal was to allow the ASD to disrupt or degrade a server that was streaming, for example, “live torture and abuse of a child” by paedophiles.

“That is not surveillance. You’ve already got the intelligence. You’ve already got the information,” Mr Pezzullo told Senate estimates last year.

“It might be done at the request of a law enforcement authority that says, ‘We can’t identify who the administrator is, we can’t identify who’s controlling this, but we know where the server is – fry it, attack it. Can you act – not surveil?’.

“I’ll use the two examples that [Home Affairs Minister Peter] Dutton limited himself to: can you, for instance, interfere with, disrupt or degrade a server that is streaming the live torture and abuse of a child? That is not surveillance.”

In London, Prime Minister Scott Morrison said the investigation was continuing.

“It’s an ongoing matter for the AFP, they’re the best to comment on that matter,” he said.

“These are matters for the AFP and not the government.”

Mr Morrison was then asked if he was troubled by police raids on journalists’ homes.

“It never troubles me that our laws are being upheld,” he said.

“Australia believes strongly in the freedom of the press and we have clear rules and protections for the freedom of the press. There are also clear rules protecting Australia’s national security and everybody should operate in accordance with all of those laws passed by our parliament.”

Last year, it was Mr Pezzullo who first confirmed – in evidence to Senate estimates – the matter was the subject of a criminal investigation.

Mr Pezzullo expressed his displeasure at the report in an opening statement to Parliament.

“It was always going to be the case, I suspect, that misinformed commentary was going to surround the establishment of Home Affairs,” he said.

“That is a price of a free press, which most certainly has to be free, but that does not, regrettably, guarantee that it has to be informed, accurate or concerned with facts.

“The worst early example of ill-informed reporting regarding Home Affairs – and this is a prize for which there were, unfortunately, many nominees – was the effort by the correspondent of The Sunday Telegraph and associated Sunday papers, who reported on Sunday, 29 April and again on Sunday, 6 May, 2018, that I had asked the Secretary of the Department of Defence and the Director of the Australian Signals Directorate to consider an increase in ASD’s powers to collect intelligence on Australians or to covertly access their private data without warrant or authorisation.

“This assertion is completely false.”

Mr Pezzullo said that “without confirming or denying the existence or content of the specific documents which the correspondent claims to have seen, I can inform this committee that I have not proposed and nor would I ever propose that ASD’s powers be expanded in the way described in this false reporting”.

“Had the correspondent bothered to check, she would have informed herself that ASD has been given, in law, a second important function which relates to the conduct of cyber-operations, which as a discipline, is quite distinct from signals intelligence collection.

“The only matter in issue in terms of potential new powers and functions, as the Minister for Home Affairs has since indicated publicly, is whether ASD’s capabilities could or should be employed in the disruption of cybercrime where the whole or parts of the relevant cyber network are hosted on Australian telecommunications infrastructure, and secondly, whether ASD’s capabilities could or should be employed in the active defence of certain critical national infrastructure networks.”

Mr Pezzullo was grilled by Labor Senator Murray Watt about “what exactly was wrong” in the report.

“The whole article,” Mr Pezzullo replied.

“The whole article?” Senator Watt said.

“Yes,” Mr Pezzullo said.

“It was falsely premised. Without referring to the legislation that this parliament has passed, it presumed that the Australian Signals Directorate … solely collects signals intelligence.”

“The correspondent says she’s seen certain documents. I know what’s in those documents. And what’s reported in the newspapers is totally at odds with what’s in those documents.

“I’m not going to comment on specific documents that may or may not exist in the terms described in the article, may or may not be drafts, may or may not now be the subject – or, in fact, are the subject – of a criminal investigation to the extent that they represent an unauthorised disclosure contrary to the Criminal Code and the Crimes Act. Setting that aside, I say emphatically and categorically to this committee there is no such proposal to expand the signals intelligence collection authorities of ASD against Australian citizens. Absolutely.”

However, Mr Pezzullo did confirm that the government was always looking at any gaps in the regime.