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While Kishimoto is the author of Naruto, there is no denying the influence his editor has had over him. Kishimoto himself has openly admitted to accepting his editors decisions.
A lot of people run around here taking Kishimoto's word as gospel, but the truth is that some decisions were not even Kishimoto's to begin with. This then leaves us at the inevitable question. What is canon?
The Naruto story itself is fundmentally not a decision Kishimoto made. Yes, the Naruto manga you know so well is actually an adaptation of Kishimoto's original idea (the pilot chapter was scrapped).
If canon is a thing that Kishimoto came up with, then the Naruto manga is fundamentally not canon.
If canon is a thing that simply credits Kishimoto as an author, then the Naruto manga, Road to Ninja, and Naruto the Last etc are all canon.