Quagliarella has reportedly been told he won't be training with the first team squad for the remainder of the season.
"It is not true," general manager Marotta told ANSA.
"He trained in the gym because he has flu and will return to training with the group as soon as possible.
"We never considered freezing him out because there is absolutely no reason to do so."
Quagliarella has been left out of Juve's Europa League squad.
Marotta continued: "I don't believe agents and the entourage of a player have the right to comment on technical choices or those of a club, so I consider (Beppe) Bozzo's comments to be out of place.
"Quagliarella is our player and has always been appreciated for his work and contribution to the team.
"The rules of international competition mean we are forced into choices that may well be unfortunate, but forced upon us.
"His absence from the UEFA list should not be considered a lack of respect, because it really wasn't, and that is proved by the fact the player was warned of the situation beforehand."
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