In Question Time, Mr Morrison also likened the commission to a “kangaroo court”.
The prime minister had been asked by Opposition Leader Anthony Albanese why he had not acted to create a federal anti-corruption commission.
In his answer, Mr Morrison decried the “shameful attacks” on Ms Berejiklian.
The former premier was brought into an investigation connected with her romantic relationship with disgraced politician Daryl Maguire.
Questions were asked whether she inappropriately pushed for funding for Mr Maguire’s pet projects in his hometown of Wagga Wagga.
“What was done to Gladys Berejiklian, the people of NSW know, was an absolute disgrace,” Mr Morrison said.
“I’m not going to allow that sort of a process, which seeks to publicly humiliate people on matters that have nothing to do with the issues before such a commission.
“The Australian people know that the former premier of NSW was done over by a bad process.
“I’m not going to have a kangaroo court taken into this Parliament.”
Mr Morrison said ICAC abused its power.
“These matters should be looking at criminal conduct, not who your boyfriend is,” he said.
“Criminal conduct is what this should look at – not chasing down someone’s love life.”
Ms Berejiklian resigned as premier last month.