UFC president Dana White says the 29-year-old Whittaker, who has a record of 20-4, became ill Saturday night and complained of pain in his abdomen before being diagnosed at a hospital with a hernia.
He later said Whittaker would be undergoing surgery on Sunday for the problem.
This marks the second time that Whittaker has been slated to fight in Australia, but been unable to compete because of complications.
The UFC confirmed the news in a press release on Sunday morning.
Despite being elevated to the main event, Adesanya's bout will remain a three-round fight.
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According to UFC officials (via MMAJunkie) Whittaker came down with a "severe abdominal injury" that will keep the middleweight champion from defending his title tonight.
It is unclear how long Whittaker will be inactive, but Gastelum's manager Ali Abdelaziz has said that he would like his fighter to face the victor of Adesanya vs Silva.
On Twitter, Gastelum also wished Whittaker well in his recovery.
Whittaker last fought Yoel Romero in a five-round war at UFC 225 in Chicago.