Naitanui hasn't featured at all this year after being grounded by an Achilles issue during the pre-season.
What started as a short-term injury ballooned into a long-term problem.
Up until last week, West Coast were hopeful Naitanui would be able to return at the tail-end of the campaign.
But Eagles coach Adam Simpson revealed on Wednesday that Naitanui's season is now officially over, with surgery expected to take place next week.
"I'm not fully across the magnitude of the surgery, but I know it's something you can fully recover from," Simpson told reporters on Wednesday.
"I know it's a long stint out, so the season is (over).
"I think it's got to the point where it needs surgical intervention to fix it."
Simpson is hopeful Naitanui can return in 2024.
"Hopefully we can get this right and he can work through the rehab and we can see him next year," he said.
"This came out of the blue a bit in the pre-season."
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