The Ivorian was forced off with a hamstring injury in the second half of City's defeat to Spurs on Saturday.
The 32-year-old has received criticism in the past over his work ethic but an improved start to the season seemed to have silenced the doubters.
But Neville believes Toure can't play three matches in a row any more and needs to be managed like Steven Gerrard, Paul Scholes and Ryan Giggs were in the latter part of their career.
He said: "He cannot play three games a week, that man.
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Yaya Toure's work ethic has come under scrutiny
"He's a fantastic player, but I would leave him for your most important games.
"There is a problem around Yaya Toure. On his day, he's perhaps the best central midfield player in the Premier League.
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"But the idea that you can get three equal performances out of him in a week now is impossible.
"We've seen it with (Steven) Gerrard, (Paul) Scholes, (Ryan) Giggs, these players that have maximum impact in teams.
"They get into their 30s and physically you drop off; you have to manage them."