The former United midfielder reportedly slammed the Premier League champions' medical team, claiming that they treated him like a guinea pig during his recovery to full fitness.
“Manchester United is disappointed with Owen’s remarks after the game on Wednesday," the club said in a statement. "The club gave him the best possible care for three years and is as disappointed as anyone he was not able to play a part in the team’s success at that time.
“It has shared all the medical records with Manchester City and is comfortable with the actions taken by its medical staff at each step of his many attempts at rehabilitation. United does not acknowledge any validity in the comments Owen is alleged to have made.
“Manchester United has some of the best sports medical staff in world sport, who have made a significant contribution to United’s on-pitch success in recent seasons.”
The 30-year-old scored his first goal for new side Manchester City during the club’s 2-0 win against Birmingham City in the third round of the Carling Cup.