Stoke City's manager says he has not told Bojan his career at the club is over.
He admits that the Spaniard has been disappointed with a lack of game time, and the two had agreed he might look for a fresh challenge.
Jones told stokecityfc.com: “As is normal at the end of every season I have had honest and amicable conversations with several players, including Bojan, about the direction we want to move forward but, contrary to reports, none of them have been told that they don’t have a future with us.
“Bojan has been excellent with me since I joined the Club in January. I’ve got a great relationship with him but, for one reason or another, things have not worked out as well as we both would have hoped.
“We were honest with each other. Bojan has been frustrated at his lack of game time and he suggested that it might be better if he looked for a fresh challenge elsewhere at this stage of his career and I agreed with him.
“But to suggest that I’ve told him he has no future at the Club is ludicrous. Quite frankly the way this has been presented is wrong.
“Bojan has been a wonderful servant for Stoke City and he will be welcomed back with open arms next season if another opportunity doesn’t arise for him.”