Home Affairs Minister Peter Dutton has attacked the integrity of a key crossbench Senator over comments he made about press freedom in the wake of two Australian Federal Police raids on journalists.

In a spiralling day of claim and counter-claim on Tuesday Senator Rex Patrick accused the powerful head of the Home Affairs Department, Mike Pezzullo, of trying to intimidate him by calling him directly to complain about his commentary about the raids on the ABC headquarters and a News Corp journalist's house.

Centre Alliance senator Rex Patrick accused Mike Pezzullo of trying to intimidate him. Credit:Dominic Lorrimer

Prime Minister Scott Morrison said he regarded Mr Pezzullo's phone call to be "concerning" and said Home Affairs Minister Mr Dutton had counselled his top bureaucrat through "an appropriate conversation".

Mr Dutton confirmed this in a written statement but then turned both barrels on Senator Patrick, despite the delicacy of current negotiations in getting the government's tax package through the upper house.