The superstar has been linked with a move away from the La Liga giants despite being contracted until mid-2018.
Bartomeu said the recent tax case against Messi, who was cleared, had an impact on the 28-year-old, but he feels the Argentina international will stay at Barca.
"Leo and his father said they don't imagine playing at another club than Barcelona," he told 8TV.
"The relationship with the family is very good. We are not in the negotiation phase yet, when the time comes it will be presented. He has contract for the next three seasons.
"Messi is very angry about the Spanish taxation. It is not normal the information published on Leo Messi. If his tax advisers have made a mistake they have to pay like everyone else. Messi deserves respect as all."
While Messi's contract is yet to be renewed, Barca are in the process of extending Neymar's stay.
Bartomeu said that was still a work in progress despite the Brazilian also having almost three years left on his deal.
"On the renewal of Neymar, this is the season of his renewal, yes," he said.
"But of course we try not to relay the negotiations and work quietly to be able to announce the extension of his contract."
