Thaksin told City's website: "There is absolutely no truth to this story or any of the allegations.
"I appreciate the progress and performance of the whole squad, managed by Sven-Goran Eriksson, this season."
On Thursday Thaksin dined with Eriksson and City players in Bangkok, where they face a Thai All Star team on Saturday.
Thaksin added that the claim that deputy chairman John Wardle had apologised to players for selling the club was "without any foundation".
A Manchester City spokesman said the club was considering legal action over the claims.
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