Begovic has been linked with a move away from the Britannia Stadium this summer, with Chelsea making at least one bid for the Bosnian.
It looked as though there had been a development when he was left out of Stoke's Carling Cup squad to face Shrewsbury and Potters chief Tony Pulis said after the game that Begovic had refused to play.
However, the former Portsmouth stopper has been in touch with the PFA to deny that was the case and insist he simply told Pulis his mind was not right to play.
PFA deputy chief executive Bobby Barnes said: "The PFA would not condone a player refusing to play for his club.
"But Asmir was at great pains to make it clear to me and the wider public that at no stage had he actually said that he refused to play for the club.
"I think it's common knowledge now that there has been a bid received.
"From Asmir's point of view he says that he had a conversation with the manager in which he was asked whether he was 100% fit and ready to play.
"Asmir's take is that he had indicated that his mind was a little bit scrambled by things and that probably if there was an alternative it would be best if he didn't play.
"But he is at great pains to say at no stage did he say that he wouldn't play, and had he been asked to play he would have done so."
Barnes added on Sky Sports News: "Managers will ask players - whether it be to do with an injury or a personal issue - is it something that you think you can clear your mind of and be able to play 100%? A player would give an honest answer to that.
"In this particular case - and I haven't spoken to Tony, who might have an alternative view - Asmir was adamant that he would have played if he was asked to play.
"But the question was 'are you 100% able mentally to play?'
"The answer has been a negative one and on that basis the manager has made a decision."
Stoke chairman Coates, meanwhile, says the club remain determined to keep hold of Begovic.
"This is an internal matter - and we will decide on what action to take," he told Sky Sports News. "Asmir Begovic remains our player.
"He is regarded as one of the best young goalkeepers in the Premier League and we are not interested in any new offers from Chelsea.
"We are not interested in what Chelsea do and we have already rejected an offer, from them, for Begovic.
"We wouldn't welcome another bid from Chelsea and, as far as I am aware, we have not received a new offer from Chelsea for him."
Stoke signed the 23-year-old for a knock-down £3.25m just before the January transfer deadline as cash-strapped Pompey were desperate to raise funds to make sure they stayed in business.