Messi's contract expires in the summer of 2021 and a report from Cadena SER earlier this month claimed the Argentine attacker was ready to walk away from Camp Nou.
But Bartomeu, who last week said he sees Messi at Barca for 'many years to come', has reiterated his belief that the six-time Ballon d'Or will extend his deal.
"Leo Messi fits in with what Barca want to do in the next few years," he told TV3.
"His contract ends in June next year and he's in peak form to be able to play for two or three more years.
"I'm sure he will renew. I have no doubt that he will continue."
The Barca captain is believed to be unhappy at a series of problems with the board in recent times, excluding leaks to the media, and waiting to see what happens in next summer's presidential elections before he commits to a new deal.
However, Bartomeu said: "Our relationship is fluid and he is not angry.
"What happened with the wage reduction is that some people at the club talked too much, but they aren't here any more."