Everton signed Stones from Barnsley in January 2013 for an undisclosed fee, understood to be £3million - and turned down a reported offer of £37million for the England defender from Chelsea during the summer.
"I laugh when people say we paid £3million for John Stones
It was £1.25million," Moyes told Sky Sports' Goals on Sunday
"It was in the January and the last signing of the window
We were trying to bring a striker in that we needed but we didn't have the money."
Barnsley have expressed their disappointment in Moyes' assertion and released a statement on their official website following an angry response from their supporters.
"Barnsley FC has been asked by a significant number of fans to clarify the situation regarding the recent comments made by David Moyes on Sky Sports' Goals on Sunday and attributed to him on the Mirror website on 14 February 2016 and elsewhere, regarding the fee paid by Everton for the transfer of John Stones from our club," the statement said
"Ordinarily, we would not comment on matters of speculation, but the article on the Mirror website carries the headline, 'David Moyes reveals Everton paid just £1.25million to sign John Stones from Barnsley'.
"The amount paid by Everton to Barnsley is Commercial in Confidence, and we would have expected that David Moyes would be bound by that obligation of confidentiality to his former employer.
"However, given the categoric nature of the assertion made, it is incumbent on Barnsley FC to correct such a statement when it is markedly and unequivocally wrong and yet is made by someone that the public might think is authoritative on the subject.
"This is particularly the case since he has cited the same erroneous fee on previous occasions also
David Moyes played no part in any negotiation with Barnsley FC concerning the transfer of John Stones, which may explain why he is mistaken as to the fee paid."
Source : PA
Source: PA