Senate crossbencher Rex Patrick claims Home Affairs boss Mike Pezzullo sought to intimidate him, alleging the senior bureaucrat wanted to silence his criticism of the nation's powerful security department.

Key points: Senator Rex Patrick believes Home Affairs Secretary Mike Pezzullo wanted to stop his criticism of the department

Senator Rex Patrick believes Home Affairs Secretary Mike Pezzullo wanted to stop his criticism of the department The crossbencher says Mr Pezzullo and Peter Dutton "hate media scrutiny"

The crossbencher says Mr Pezzullo and Peter Dutton "hate media scrutiny" Mr Pezzullo denies those suggestions, taking issue only with the senator's personal criticism

But Mr Pezzullo strongly rejected Senator Patrick's claims, saying he had only asked the South Australian parliamentarian to "reflect" on his "unfounded" comments made in the wake of federal police raids on the home of News Corp journalist Annika Smethurst and the ABC last week.

The crossbencher issued a statement last Tuesday on the search warrant executed on Smethurst's Canberra home, stating that "Home Affairs Minister Peter Dutton and Home Affairs Secretary Mike Pezzullo clearly hate media scrutiny".

Senator Patrick, who was also interviewed on the ABC's RN Breakfast about the raids, received a request from Mr Pezzullo's staff to discuss the matter.

"When (Mr Pezzullo) called me, he basically stated that he was concerned with remarks that I had made on Fran Kelly's show and indeed remarks that I had made in a press release that criticised him personally," Senator Patrick said.

"He considered that the remarks had a slanderous element to them. He was very quick in stating that he wouldn't be pursuing that.

"But basically he stated to me that, as a senator, I sit in high office and it's a bit unfair for me to criticise someone like him when he has no opportunity for rebuttal."

Senator Patrick described Mr Pezzullo as "polite but firm" during the conversation, which was their first outside of committee hearings, but said he has since formed an opinion of the Home Affairs Secretary's motives.

"I've tried to reconcile in my mind what the phone call was about, and the only thing I can think of is that he was trying to get me to be quiet in respect of my criticisms of the Department of Home Affairs," he said.

"As a senator, I have a responsibility for oversight of government, and I won't be constrained in what I say about ministers or indeed secretaries if I think that they're not acting in the best interests of their constituents."

Pezzullo claims comments 'unfounded'

Mr Pezzullo strongly denied the crossbencher's suggestions.

"I have no view and nor should I express a view on how Senator Patrick conducts himself or on the issues that he chooses to pursue as a senator," Mr Pezzullo told the ABC.

"My sole request made to him by telephone was to ask that he reflect on his adverse references to my purported view of media scrutiny."

"His comments were unfounded and not able to be responded to by me in the media as quite properly I lack the public platform that he has, and uses."

The Home Affairs Secretary argued he also took the opportunity to point Senator Patrick to questioning he had been subjected to in Senate Estimates in May 2018, one month after Smethurst's story was published.

"I was very grateful that he took my call and appreciative of the fact that he undertook to consider my representations, which of course he was under no obligation to do," Mr Pezzullo said.

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Greens senator Jordon Steele-John took to social media to reveal he was also contacted by Mr Pezzullo, after criticising him in Parliament during the debate over new encryption laws last year.

It is understood that was by a letter to Senate President Scott Ryan, which the Secretary copied Senator Steele-John into, where he raised similar concerns about attacks on his reputation.

The South Australian crossbencher said he would not be changing his approach to his job as a result of his chat with the Secretary.

"I've got pretty broad shoulders, I'm a former submariner, I've lived in an environment of sharks — and much bigger sharks than Mr Pezzullo," Senator Patrick said.

"However, I do think it's inappropriate for a secretary of a department to contact a senator, for the purposes of trying to prevent them from raising criticism of a department."