The network decided to cut ties with its long-standing breakfast show presenter on Wednesday, Nine newspapers report, following the release of a now-deleted podcast interview with a British far-right activist that landed Stefanovic in hot water with his employer.
The host of the Nine Network's flagship Today show interviewed controversial anti-Islam figure Tommy Robinson, saying he admired Robinson's "tenacity" and "courage".
The almost-hour-long episode of The Karl Stefanovic Show, which is run independently of Nine, was published on Tuesday evening but was pulled down by the following morning.
However, the episode was resurrected on YouTube by Pauline Hanson, who Robinson praises several times during the interview.
Earlier on Wednesday, Nine made its strongest statement about Stefanovic's contentious foray into podcasting, saying it was taking his most recent episode "seriously".
"The Karl Stefanovic Show is a completely independent production," a Nine spokesperson told AAP earlier on Wednesday.
"Nine has no involvement, including in the guest selection and other editorial processes.
"However, Nine is taking this matter seriously."
Stefanovic described Robinson as one of Britain's "most controversial public figures" in a segment at the beginning of the podcast.
"I really do admire your tenacity and the courage that you're showing in trying to stand up for what you believe is right," he said during the interview.
Why the episode was taken down or who made the call is not yet known, though it has been removed from Stefanovic's YouTube channel, Spotify and Apple Podcasts.
The One Nation leader posted the video on her YouTube channel on Wednesday morning, claiming Nine was "trying to sack my good friend Karl Stefanovic".
Robinson, whose real name is Stephen Christopher Yaxley-Lennon, is a prominent far-right activist and founder of the anti-Islam English Defence League movement.
He has been banned from several social media platforms for violating rules on hateful conduct and hate speech and has multiple criminal convictions.
During the roving discussion, the pair touched on populist, far-right politics in the UK, the US and abroad.
"I love her, Pauline," Robinson said of the insurgent One Nation leader, the first guest to be featured in the inaugural episode of Stefanovic's podcast.
"She's been through what I've been through: she's been condemned, attacked, battered, every name under the sun.
"And here she is, she's carried on against all of that backlash."
While the full interview has been scrubbed, a promotional clip and an interview snippet remain active on Stefanovic's X account.
In one clip, Robinson speaks to the costs of speaking out about immigration and Islam, touting his own experience being deplatformed from social media.
Stefanovic opened the interview by saying: "I'm surprised you're not dead yet".
The pair are seen walking side by side, Robinson wearing a "unite the kingdom" T-shirt, the name given to a series of large-scale anti-immigration rallies in London.
Prompted to finish Robinson's sentence, Stefanovic describes Keir Starmer, the outgoing UK Labour prime minister, as a "wanker".
"We speak to Tommy Robinson. The guy you've all been asking for," the caption reads.
"The ultimate disruptor. Many say, a voice for the people."
Stefanovic has been contacted for comment.
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