Mr Perrottet dismissed claims from Liberal MP Jason Falinski that the people of NSW had discounted the Independent Commission Against Corruption, which is investigating former premier Gladys Berejiklian.
“Ultimately, what we should be doing is instilling confidence, not taking it away.”
Mr Perrottet said ICAC had a strong and important role in NSW’s future.
It came as federal Liberal frontbenchers threw their weight behind a possible return to politics for Ms Berejiklian, who resigned voluntarily after it emerged she was under investigation by ICAC.
She has also been accused of turning a blind eye to Mr Maguire’s corrupt conduct.
The idea Ms Berejiklian might run as the Liberal candidate in the federal seat of Warringah has dominated the media cycle for two days.
“The way that Gladys Berejiklian has been treated has been shameful,” he said.
“I don’t call that justice.”
But by Wednesday, Mr Morrison was backing away. He said Ms Berejiklian would make a strong contribution to his federal team if she decided to run despite the ICAC probe – an investigation he has also dismissed as a kangaroo court.
“That’s a decision for Gladys, ultimately, and she may choose not to go ahead here, I suspect,” he said in Sydney.
“That’s a matter for her and I respect her choice.”
Mr Morrison said Ms Berejiklian had had a difficult time due to the anti-corruption inquiry, which grilled her on details of her private life.
“I know it’s been a very difficult time for her in recent times,” he said.
“She has suffered terribly in terms of things that have been aired publicly and I think that was just awful to watch.”
Ms Berejiklian is yet to make any public comment on whether she is considering a federal tilt.
Labor MPs have criticised Mr Morrison for dismissing the NSW investigation and for casting doubt over the ICAC’s independence.
Warringah MP Zali Steggall said integrity was a major issue in her electorate and chastised government ministers for being out of touch with the public by continuing to undermine the ICAC.
The independent also said she remained confident of her position in the Sydney seat. Any Liberal candidate would be a puppet of Barnaby Joyce on climate policy, which is a key issue in Warringah, she said.