Senior public servant Mike Pezzullo telephoned AFP Deputy Commissioner Neil Gaughan to compliment him on the police raid on the home of News Corp journalist Annika Smethurst.

Key points: The phone call has led senator Rex Patrick to question the judgment of Mr Pezzullo

The phone call has led senator Rex Patrick to question the judgment of Mr Pezzullo The documents were obtained under Freedom of Information

The documents were obtained under Freedom of Information Mr Pezzullo said it was inaccurate to conflate professional compliments to colleagues with "a supposed attitude to press freedom"

Newly released documents revealed that in an email sent to staff on the evening of the raid, Mr Gaughan said:

"Good work by all involved. I also received a call this evening from the Sec DHA [Secretary of the Department of Home Affairs, Mr Pezzullo] who is fully supportive of the actions of the AFP and ask [sic] me to pass on my [sic] thanks to the team involved. "Well done — tomorrow is another day."

The phone call has led South Australian senator Rex Patrick, who obtained the documents, to question the judgment of Mr Pezzullo.

The documents, obtained under Freedom of Information, shed more light on the June 4 raid on the home of Smethurst and the raid the following day on the ABC's Sydney headquarters — which the documents showed the AFP named Operations Woolf and Klasies, respectively.

"The contents of the released documents confirm a lack of judgment at the highest levels of Home Affairs where national strategy and security policy is set," Senator Patrick told the ABC.

"After the raid on Ms Smethurst, alarm bells immediately started ringing for the media, the public, and indeed across government.

"Yet the Secretary of Home Affairs appears to have been blind to public concerns, expressing satisfaction with the raids."

Approached this week by the ABC, Mr Pezzullo confirmed he had made the call to Mr Gaughan.

Federal Police raided News Corp journalist Annika Smethurst's house following a story she wrote a year ago. ( ABC News )

Asked whether it was appropriate for a senior public servant to express full support for the AFP on an operational matter, Mr Pezzullo said:

"DC Gaughan is a colleague. In the discussion in question, I expressed my compliments to him and his officers on their professionalism and their diligent focus on independently enforcing the laws of the land, as the Parliament has passed them.

"To conflate the expression of professional compliments to colleagues with a supposed attitude to press freedom is not an accurate comparison.

"As per my evidence to the PJCIS [Parliamentary Joint Committee on Intelligence and Security], I was surprised that Ms Smethurst was under investigation and had put the matter out of my mind until DC Gaughan advised me the AFP was in the process of executing the warrant."

Mr Pezzullo referred the ABC to his evidence to the PJCIS which he said addressed the public service working collaboratively with the media to ensure the media could safely, and without endangering sources, establish what was "protected national security information" where lives or crucial capabilities might be at risk.

On August 14, Mr Pezzullo was asked at a PJCIS hearing what he would do if a media organisation came to him with a leaked government document.

He replied that from real-life experience, which had resulted in stories subsequently being produced, there was always scope for negotiation.

"In a sense, you don't really need to talk about the detail of that weapons system or the capabilities of our submarines or how ASIS goes about its business, but you've got the document," he said.

"I might not like the fact that you've got the document, and that goes to the separate question of who the primary discloser is. How is it that the document came to be in the possession of the reporter or the person involved in the news business otherwise?

"But I accept, in a country with a free press, they're going to publish. So, how is it that you can steer, assist and work with that journalist to ensure that lives are not put at risk, that sources and methods are not compromised?

"It might be that the point of the story they're trying to get at is human rights abuses or maladministration or other facets that are in the public interest, where the capabilities themselves or the systems that we rely upon to keep our country safe don't gratuitously need to be retailed."

But Senator Patrick said at no time since the raid on Smethurst's house and then on the ABC's Sydney headquarters had Mr Pezzullo conceded publicly that the balance between national security and media freedom was not struck in those raids.

He said Mr Pezzullo's own minister, Peter Dutton, had since the raids issued a ministerial directive requiring the AFP to consider media freedom before taking any action against a media outlet.

"Instead, under media and public pressure, Mr Dutton has had to sidestep him [Mr Pezzullo] and issue ministerial directive ordering police to consider the importance of press freedom before investigating reporters," Senator Patrick said.

"I fear Mr Pezzullo is too close to the trees to see the forest, and that's not good for the secretary of a department. Secretaries must be able to stand back and view things objectively from a total public policy perspective."

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