Ms Flint broke down in tears as she reflected on her time in parliament, including aggressive and sexist conduct during the federal election campaign in 2019.
The prime minister said Ms Flint was incredibly brave to speak out about her experience.
"I was there with her as she endured one of the ugliest campaigns I've ever seen waged against not just a woman but anyone in this country," he told reporters in Canberra on Wednesday.
"Her determination to stand up to that in the face of the most vitriolic abuse, stalking and threats to her own public security, it was just absolutely appalling."
Mr Morrison accused Labor, the unions and activist group GetUp of standing by and letting it happen. However, each group has vigorously denied any connection to the harassment of Ms Flint and condemned the way she was treated.
Ms Flint, who will quit politics at the next election, says the workplace culture inside Parliament House needs to change in relation to the treatment of women.
While much of the focus has centred on allegations of sexual harassment and assault within the Liberal Party, she said Opposition Leader Anthony Albanese needed to get his own house in order.
The member for the South Australian seat of Boothby said Labor leaders should have stood up and supported her when they saw what she was subjected to during the 2019 campaign.
"The safety of women in this place of female staff, of female MPs and senators, should be above politics," she told parliament on Tuesday night.
"The need to change the culture of our parties and of this place should be above politics."
Ms Flint said she would not be lectured to by Labor MPs about the treatment of women.
"I ask the leader of the opposition, where was he and where was his predecessor and where were the senior Labor women when GetUp, Labor and the unions' supporters chased, harassed and screamed at me, everywhere I went in the lead-up to the 2019 election?"
She said all sides of politics needed to deal with the issue through an independent review by Sex Discrimination Commissioner Kate Jenkins.
Mr Albanese said Ms Flint deserved to be safe and people should listen to her story.
"We must learn to have disagreements in a civil way," he said.
"Such behaviour from anyone towards a woman or anyone else in politics is completely inappropriate and should not happen."
Mr Albanese's office was also targeted during the 2019 campaign, intimidating his female staff.
Opposition frontbencher Penny Wong said the harassment and abuse Ms Flint experienced was utterly unacceptable but it was unfair to criticise Labor women for it.
"I would say to Ms Flint, I agree with you, let's work together to make this a better place for women," Senator Wong told reporters.
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