The home affairs minister Peter Dutton said it was “inappropriate” for his departmental secretary to contact a senator who was critical of the government’s handling of press freedom.

The remarks come shortly after prime minister Scott Morrison weighed in on the matter, calling it “concerning” Mike Pezzullo allegedly attempted to silence Centre Alliance senator Rex Patrick.

But Dutton said he understood Pezzullo’s impulse in making the phone call, characterising Patrick as someone who would “seek to misrepresent” what he was told.

“Secretary Pezzullo and I discussed the matter this morning,” Dutton said in a statement published by the ABC.

“Like me he is disgusted at some of the outrageous lies and slander he and I are regularly subject to, but nonetheless, I advised the secretary it was inappropriate to contact Senator Patrick, even if just to point out the inaccuracies in the senator’s press release.

“Further, I advised it was counter productive because I have always found Senator Patrick to be a person of the sort of character who would seek to misrepresent the Secretary’s words, and the Secretary agreed the contact was not appropriate and that is where the matter ends.”

In response, Patrick said he found Dutton’s comments to be unhelpful to the debate.

“I work constructively with ministers and government departments all the time,” he said.

“Nonetheless, I understand Mr Pezzullo has been counselled and for me, that is the end of the matter.”

Pezzullo has strongly rejected the suggestion he sought to intimidate Centre Alliance’s Rex Patrick, but acknowledged that he asked him to reflect on his “unfounded” comments in the wake of federal police raids on the ABC and News Corp journalist Annika Smethurst’s home.

Morrison earlier told reporters in Sydney: “I do find those things concerning,” adding that he had discussed the incident with the home affairs minister who “has had an appropriate conversation with the secretary”.

Political fallout from the raids is set to continue, with calls from independent MP Andrew Wilkie for a parliamentary committee – to include minor parties and independents – to review national security laws.

Labor has also accused the government of secrecy and called for a bipartisan push to review national security laws but declined to nominate any concrete changes it will pursue to improve press freedom.

On Tuesday Morrison suggested that “press freedom is essential to our democracy” while warning that “no one is above the law”.

He noted that the raids were conducted under the Crimes Act as in-force in 2017 and 2018, before the espionage bill added a defence for journalists where they “reasonably believe” dealing with secret information is in the public interest.

Morrison said if there was “evidence or any analysis that reveals there is a need for further improvement of those laws, the government is open to that” – without endorsing calls for a fresh review.

Patrick has been one of the fiercest critics of the raids, including suggesting there is a double standard with leaks embarrassing to the government pursued more vigorously than others, and claiming that Pezzullo and Dutton “clearly hate media scrutiny”.

Patrick revealed in a post on Facebook that Pezzullo called him to complain about those comments.

“Pezzullo suggested these remarks had ‘slandered him’, though he quickly indicated he would not take that any further, before remonstrating with me for making my remarks from my position of ‘high office’ in circumstances in which he claimed he had no real ability to respond,” Patrick wrote.

“He took the view that while I was in my rights as a senator to comment about and indeed criticise his minister, Peter Dutton, I should refrain from commentary about him, the secretary of home affairs.”

The Greens senator Jordan Steele-John revealed that Pezzullo had also personally complained to him regarding criticisms of the encryption bill and “the secrecy of his department”.

Interesting to hear this morning that Mike Pezzullo has personally complained to @Senator_Patrick



He did the same thing to me over my criticisms of the #AAbill and the secrecy of his department #Auspol — Senator Jordon Steele-John 🧻💧 (@Jordonsteele) June 10, 2019

Patrick told Guardian Australia that Pezzullo was “polite” and “not aggressive or rude” but felt pressure when he “reflected on the purpose” of the call to stop his public criticism.

Patrick said the phone call “from the chief bureaucrat overseeing a national security juggernaut, effectively a ministry of state security” left him with “the distinct impression of a menacing tone in his remarks and an unmistakable message that criticism and scrutiny is not welcome”.

“In a quiet but significant way I was the subject of the next stage of oversight clampdown where the apparatus moves from intimidating the media, who are charged with the responsibility of informing the public of questionable conduct by government officials, to intimidating members of the parliament who have a constitutional responsibility to oversight government.”

In a statement to the ABC, Pezzullo said he had “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”.

“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,” he reportedly said.

“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.

“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.”