Barca announced earlier this week that the four-time Ballon d'Or winner would not play for "six to eight weeks" with a hamstring injury, ruling him out of the rest of the year.
It is the third injury of its kind the 26-year-old has suffered this season and it was added that Argentinean doctor Luis Garcia would work with him on his recovery.
But as Garcia is not a Barcelona employee, it led to media speculation that Messi had taken umbrage with his club's medical staff and in particular, physiotherapist Juanjo Brau, over the recurring nature of his problem.
However sporting director Andoni Zubizarreta said of Garcia that "he is very well known to our medical staff" and Messi's management went one step further to play down the rumours of a fall-out with a man he was worked closely with in the past.
"The process of recovery from the injury suffered last Sunday during the game Betis v FC Barcelona began on Monday November 11," said a statement from Leo Messi management which was carried by Spanish newspaper Marca.
"This injury, although of the same type and to the same leg, is not related to any previous ones. From two days ago the medical services of Futbol Club Barcelona are treating him so that he can recover completely.
"Being a player of the Asociacion de Futbol Argentino [AFA], and having games programmed with the national team, the licensed kinesiologist Dr. Luis Garcia arrived yesterday in Barcelona to represent the national team, to monitor the injury, and to know the state and scope of the same.
"Barca's medical services, as always, are those who take charge of accompanying him and treating him, like any other player at the club in other occasions.
"So they will be supervising his injury during the whole process, including when Leo travels to Argentina during the Christmas period.
"We want to deny completely the information published in some media, and confirm the comments of different club figures: Juanjo Brau, a great professional who has been close [to Messi] for a long period of time in recent years, no longer works day-to-day with Leo because FC Barcelona promoted him professionally.
"His current responsibilities are coordinating the club's first team squad physios.
"There have been no professional or personal differences, nor a distancing outside of not being as close during their daily work."