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 interview with British anti-Islam figure Tommy Robinson that landed Stefanovic in hot water with his employer.
The host of the Nine Network's flagship Today show interviewed Robinson in an almost-hour-long episode of The Karl Stefanovic Show, which is run independently of Nine, saying he admired his guest's "tenacity" and "courage".
Stefanovic introduced Robinson in the interview as "one of Britain's most controversial figures".
The podcast episode was published on Tuesday evening but was pulled down by the following morning.
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."
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.
Senator Hanson posted the video on her YouTube channel on Wednesday morning, claiming Nine was "trying to sack my good friend Karl Stefanovic".
She told Sky News that Nine would be "bloody stupid" to sack Stefanovic, offering him a job with One Nation.
"They've gone so far to the left, Channel Nine, they're making a big mistake," Senator Hanson said on Wednesday night.
"Hey, guess what, Karl? I'm looking for someone in my office. I want some advisers in my office. So, Karl, come and apply for a job with me. We'll have a great time. We'll put them all on notice and we'll get the country back on track."
Robinson, whose real name is Stephen Yaxley-Lennon, was a co-founder of the now-defunct 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.
"I really do admire your tenacity and the courage that you're showing in trying to stand up for what you believe is right," Stefanovic said during the interview.
Stefanovic and Robinson discussed populist politics in the United Kingdom, the United States and abroad.
"I love her, Pauline," Robinson said of the 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."
A promotional clip and an interview snippet of the interview 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".
Stefanovic has been contacted for comment.
