Recent reports had claimed that the Spanish international had made his mind up to leave the Catalan outfit at the end of the current campaign due to concerns over a lack of starting opportunities.
Despite insisting that the coaching staff want the 31-year-old to stay, Bartomeu has said that they would not prevent any unhappy squad members from departing.
"The coaches hope he is here next season but we will not retain any player who is uncomfortable," Bartomeu told BTV. "In that case, we will talk to him to seek a solution."
Villa joined Barca from Valencia for a reported £35m in the summer of 2010.