On Tuesday, Messi shocked the Catalan side when he faxed the club requested that he be let go from his contract.
Messi's decision came after a season in which Barcelona failed to claim Silverware for the first time in 12 years, with their embarrassing exit from the Champions League at the hands of Bayern apparently proving to be the final straw for the six-time Ballon d'Or winner.
The Argentine has been with Barcelona for 20 years now, and with that in mind, Freixa disapproves of his recent transfer request.
“I am not overly concerned about Messi leaving because everything has an end," he told Radio Marca.
“What is important is that he did it in such an unfortunate way and without respecting the club.”
Messi currently has a €700m buyout clause in his contract, which he is disputing as he previously had a clause allowing him to leave for free which expired at the end of May. In the player's eyes, that remains valid due to the season being extended.
Freixa says that if Messi wants to leave, that amount will have to be paid somehow.
“I am surprised and disappointed as a Barcelona man. I am disappointed by what Messi has done," he added.
“The contracts are to be fulfilled and what Messi has to do is come with €700m and leave.”
The teams thought to be leading the race to sign Barca's greatest ever goalscorer are Inter and Manchester City.