The network reportedly decided to cut ties with its long-standing Today show host on Wednesday after the release of a now-deleted podcast interview with far-right figure Tommy Robinson, who has been accused of fuelling violent anti-immigration protests in the UK.
Stefanovic has been criticised for failing to challenge Robinson during the nearly hour-long interview, in which he praises his guest's "tenacity" and "courage" for "trying to stand up for what you believe is right".
On Thursday, Home Affairs Minister Tony Burke questioned the merit of giving a platform to someone such as Robinson.
"He certainly wouldn't get a visa under me, he certainly wouldn't get a platform under me," Mr Burke said of Robinson, who has been denied entry to Australia by previous governments.
"The last thing we need in Australia is for the temperature to be raised by people who want to spread hatred being given a louder voice."
Prime Minister Anthony Albanese weighed into the matter, telling a speaking event in Canberra: "I don't want to get into a debate about Nine at the moment, but you know, look at what's happened.
''You go down that road and you get further and further out on the edges of what is mainstream political debate in this country, and ... I think that that can have, you know, an impact."
The Karl Stefanovic Show episode was published on Tuesday evening but was pulled down from multiple platforms by the following morning.
It was resurrected on YouTube by Pauline Hanson, who Robinson praised during the interview.
The episode reportedly sparked a full day of executive crisis talks at Nine.
While the network is not involved in the running of the podcast, it has kept Stefanovic on the payroll as the co-host of its flagship breakfast program.
As pressure mounted on Wednesday, Nine took pains to distance itself from the podcast.
"The Karl Stefanovic Show is a completely independent production," a Nine spokesperson told AAP at the time.
"Nine has no involvement, including in the guest selection and other editorial processes.
"However, Nine is taking this matter seriously."
Radio giant ARN, which hosts a once-weekly podcast with Stefanovic and Eddie McGuire, has also put itself at arm's length, telling multiple outlets The Karl Stefanovic Show is independent and not representative of ARN's editorial standards or views.
The interview sparked a rebuke from activist group Mad F***ing Witches, a grassroots group known for pressuring advertisers to pull money from media outlets in its crosshairs.
The organisation has previously drained funds from the employers of shock jocks Alan Jones and Kyle Sandilands.
On Wednesday, it appeared to take credit for Stefanovic's expected departure from the network.
"Congratulations, witches," it wrote, sharing a news report. "We did it again."
It is unclear why the episode was taken down or who made the call.
However, Senator Hanson reposted the video of the episode on her YouTube channel on Wednesday morning, claiming Nine was "trying to sack my good friend Karl Stefanovic".
Nationals leader Matt Canavan also rushed to Stefanovic's defence once news broke he was set to depart the network.
"Australian journalists should not lose their jobs for talking to someone," he wrote on X.
"Reports of Karl's sacking, if true, are a win for the thought police."
Robinson, whose real name is Stephen Yaxley-Lennon, was a co-founder of the now-defunct anti-Islam English Defence League movement.
He has twice cancelled speaking tours of Australia after being denied a visa and has multiple criminal convictions.
In a video teasing the episode online, Stefanovic puts his arm around Robinson.
"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.
Stefanovic has co-hosted the Today show on and off for more than two decades, after first joining the network as a reporter in 2000.
Stefanovic and ARN have been contacted for comment.
