Walsh's early season absence is a hefty blow to the Blues' hopes of kicking on for their first finals appearance since 2013.
The club's 2021 best and fairest winner, he is a crucial part of the Carlton midfield.
Walsh had been managing a back injury since the end of the 2022 season, including missing the round 23 loss to Collingwood that cost the Blues a long-awaited finals berth.
Carlton had played down the seriousness of the setback earlier in pre-season but on Friday confirmed Walsh had a micro-discectomy procedure in his back on Thursday night.
The surgery involved the removal of a bulging disc portion to relieve pressure on a nerve.
The Blues said they had taken several months to explore alternatives for the 22-year-old before opting for surgery.
"Throughout the last few months our number one priority has been for Sam's wellbeing in managing this issue, which is why we explored every possible conservative treatment option," Carlton football boss Brad Lloyd said on Friday.
"Following this extensive process, it was clear that given all alternative treatments had not progressed his recovery, surgery was the required option to correct the issue.
"Sam is now recovering after undergoing surgery last night and will commence his rehabilitation in the New Year.
"While Sam's professionalism and resilience is well-known, we will absolutely give Sam all the time he needs to make a full recovery before he returns to the side during the season.
"Due to the long-term nature of this rehabilitation, it isn't possible to confirm a set date for his return right now.
"Once the opening month of the season has been completed though, we expect to be able to provide more clarity on his expected return to play."
Walsh has played 81 games and kicked 31 goals since he was drafted at pick No.1 in the 2018 AFL draft.
He won the AFL Rising Star award in his debut season in 2019 and was All-Australian in 2021.
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