Home Affairs Minister Peter Dutton has counselled his departmental secretary Mike Pezzullo over concerns he intimidated a crossbench senator in a phone call last week, which the Prime Minister describes as "concerning".

Key points: Scott Morrison says he was concerned the Home Affairs boss called a crossbench senator

Scott Morrison says he was concerned the Home Affairs boss called a crossbench senator He says Home Affairs Minister Peter Dutton counselled Mr Pezzullo after the call was revealed

He says Home Affairs Minister Peter Dutton counselled Mr Pezzullo after the call was revealed Mr Dutton says it was 'inappropriate' to call a senator "even if just to point out inaccuracies"

The ABC revealed Mr Pezzullo called South Australian senator Rex Patrick to hit back at personal criticism the crossbencher had levelled at him in the wake of last week's Australian Federal Police raids on the media.

Mr Morrison said such a call could be seen as inappropriate.

"Well, I do find those things concerning, and the Home Affairs Minister and I have discussed that," the Prime Minister said.

"And the Home Affairs Minister has had an appropriate conversation with the secretary."

Last week, Senator Patrick issued a press release stating Mr Pezzullo and Home Affairs Minister Peter Dutton "hate media scrutiny".

The Centre Alliance senator told the ABC he believed the only motive for such a call was to try to silence him from further criticism of the Home Affairs Department and the secretary.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Watch Duration: 1 minute 1 m Mike Pezzullo (right) denies he was trying to intimidate Rex Patrick

Mr Pezzullo strenuously denied that, telling the ABC he merely wanted Senator Patrick to "reflect" on comments that could be viewed as slanderous.

The ABC asked Mr Pezzullo about the Prime Minister's statement, however he offered no further comment.

Senator Patrick said it was the first time Mr Pezzullo had contacted him, although the two have previously sparred in Senate Estimates at Parliament House.

Mr Dutton, in a statement, said he discussed the matter with Mr Pezzullo this morning.

"Like me he is disgusted at some of the outrageous lies and slander he and I are regularly subject to," the Home Affairs Minister said.

"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 counterproductive 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."

Opposition Leader Anthony Albanese said he had a good relationship with Mr Pezzullo, but noted his duties in Parliament were different to that of a senator.

"I think that's the concern here ... given that Senator Patrick as a senator in Senate Estimates has a responsibility for grilling Mr Pezzullo and other bureaucrats to account," Mr Albanese told ABC Radio Perth.

Greens senator Jordon Steele-John said he was also contacted by Mr Pezzullo last year, after launching a scathing personal critique of him in Parliament during debate on the encryption legislation.

Mr Pezzullo did not call Senator Steele-John, rather writing a letter to Senate President Scott Ryan and copying the senator in, raising concerns about the character assessment.