A Nine staffer told the newspaper that the popular duo would have pay parity for their work on the Today show, however Stefanovic's extra responsibilities with 60 Minutes and news meant the roles are "actually not equal".
It's understood six months of talks ended on Monday with Nine bosses deciding not to renew her contract. She will instead join The Project in a senior hosting and editorial role beginning in January 2018.
Nine's Director of News and Current Affairs Darren Wick confirmed the negotiations came to an "impasse".
"We have been trying to negotiate this contract for near on six months and haven't been able to come to terms," Wick said. "After six months of negotiation both parties have made their positions clear."
According to reports, the issue for Wilkinson all boiled down to wanting pay parity with Stefanovic - who is one of the highest-paid stars on Australian television.
His salary vastly outstrips that of his Seven breakfast show rival, David Koch, who reportedly earns $1 million a year hosting Sunrise, while his co-host Samantha Armytage was reported to be on $500,000 earlier this year.
Meanwhile, it's claimed Seven's The Morning Show host Larry Emdur is bringing in around $800,000 annually.
In 2015, it was reported in The Daily Telegraph that A Current Affair host Tracy Grimshaw - one of the longest-serving stars at Channel Nine - was on $650,000.
On Monday, Nine confirmed it was "unable to meet the expectations of Lisa Wilkinson and her manager on a contract renewal for a further period".
"We express our gratitude to Lisa for her 10 years with the Today show and are disappointed we find ourselves in this position. Nine will be going in another direction and will be considering our options in the coming weeks and months."
Lisa Wilkinson has previously denied there being a gender pay gap on the Today show. She told Charlie Pickering on The Week she had not discussed pay with Stefanovic, but called "bullsh*t" on the claims.
"It's been widely reported that Karl is paid significantly more than you to host the Today show. Why do you think that is?" Pickering asked.
Wilkinson replied: "And you believe everything you read?"
Nine's CEO Hugh Marks said: "Today show is one of the biggest roles there is in television and requires an enormous commitment from its hosts."
"The partnership between Lisa and Karl has taken the show to the success it is today and we thank Lisa for everything she has done for the show and for Nine over the past 10 years. We all wish her well for the future."
