The Italian striker trained separately from his team-mates on Tuesday, just hours after his agent hit out at Juve for leaving Quagliarella out of the club's Europa League roster.
"Those reports are not true," Marotta said in quotes reported by Gazzetta dello Sport. "Fabio 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 was the only Juve player omitted from Antonio Conte's European roster ahead of this month's last-32 tie against Trabzonspor.
Juve's decision left the 30-year-old "angry and disrespected", according to the player' agent Giuseppe Bozzo.
"I don't believe agents and the entourage of a player have the right to comment on technical decisions so I consider Bozzo's comments to be out of place," Marotta said in response.
"Quagliarella is our player and has always been appreciated for his work and contribution to the team."