The three-time Olympic gold medallist has won 14 world titles, ten of them in individual events to make her the greatest women's competitor in the history of the sport.
The Australian revealed her condition last month and withdrew from the remaining World Cup events in Europe.
She had been hoping to be fit for the worlds in Sydney from September 29-October 4.
"For the first time in 15 years, I won't be on the start line at the world championships," she said on social media.
"Unfortunately, I just won't be ready in time. I need to put my health and recovery first after surgery.
"I'm absolutely devastated to be missing this one -- a world championships on my home course," she added.
The 31-year-old, the reigning Olympic champion in the women's C1 (canoe) and women's K1 (kayak), among six medals won across four Games, is also the current K1 and K1 team gold medallist.