In the aftermath of Wednesday's Carling Cup win for Manchester City against Birmingham, when Hargreaves marked his Blues debut with a goal, the 30-year-old outlined the unhappiness over sections of the treatment he received to combat a tendinitis injury he had before leaving Bayern Munich in 2007.
Hargreaves said in the end, he felt like "a guinea pig" such were the revolutionary treatments he was forced to undergo in an effort to solve a problem he felt had been exacerbated by the injections.
Sir Alex Ferguson mounted a staunch defence of his medical staff earlier today.
Now United have released a full statement, in which they dismiss Hargreaves' claims and state they remain "comfortable" with the treatment the midfielder received.
"United does not acknowledge any validity in the comments Owen is alleged to have made," said the statement.
The statement continued: "Manchester United is disappointed with Owen's remarks after the game on Wednesday.
"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.
"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."
Earlier, Ferguson was adamant any criticism of his back-room team was completely without foundation.
"Do you think we would be successful if they were not 100% brilliant? Our doctor and his five physios are fantastic - that is my opinion and that is more important than what anyone else has to say about it," said the Scot.
Hargreaves underwent surgery on both knees during the 2008-09 season.
Following the operations, Hargreaves played just six minutes of first-team football as he battled to regain fitness and was eventually released by United in the summer.
But he has achieved full fitness barely three weeks after joining City on a free transfer and claimed on Wednesday the medical treatment he received at United did more harm than good.
"I received some injections but my tendon was never the same," he said.
"After the injections, I tried to get back on my feet and they said my tendon was good, but it felt like I was made out of glass.
"With my tendon injury, I've had to be a guinea pig for a lot of these treatments. All the people there [at United] are lovely and everybody tries their best, but at times you come to a certain point where you need to make a decision.
"I wanted to play. Everyone wanted me to play, so it's not really an option to say, 'sit it out and rest for six months'. With hindsight it's a lot easier, but I wish I had not had the injections."
Aware of the delicate nature of the matter, City manager Roberto Mancini opted to tiptoe carefully through the row this morning, although he confirmed Hargreaves is now pain free.
"There are no problems, apart from a bit of tiredness," Mancini said.
"He has been out for two years, which is a long period. He has worked hard for the last six months in Canada. And I hope it has solved all his problems.
"I don't think they (United) got it wrong. I just hope he will be lucky in the next two years.
"After something like this, it can happen that after one or two games he might have a problem with his ankle or hamstring or something.
"But I remember him very well when he played for United and Bayern. He was an incredible midfielder.
"United paid £17million for him and he is 30 years old. On top form he is one of the best midfielders in Europe."