Hargreaves, who joined rivals Manchester City as a free agent in the close season after four years in the red half of the city where he made just 39 appearances, said injections he had received had hampered his recovery from knee problems.
"As far as I'm concerned... my medical staff are one of the main reasons Manchester United have been so successful in the last few years," Ferguson told a news conference.
"There is absolutely no doubt about that. We have fantastic medical staff and great sports scientists... that's my opinion of Manchester United and that's more important than what anyone else has got to stay about that."
"I received some injections and my tendon was never the same," said Hargreaves, who moved to United from Bayern Munich for 17 million pounds in 2007 despite having broken his leg.
"I tried to get back on my feet and [United's medical staff] said my tendon was good, but it felt like I was made of glass. [The injections] obviously had a huge impact. With hindsight, I probably should not have had them. It's difficult.
"I've had to be a guinea pig for a lot of treatments."
United issued a statement later in the day saying it "does not acknowledge any validity in the comments" Hargreaves made and that the club had some of the best sports medical staff in the world.
"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 said on its website.
"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."
"I think for him now it is important to play often and to train without problems, I think the past is the past," the Italian told a news conference, adding that he was "absolutely" sure United had not got the player's treatment wrong.
"I said: 'I think I've got a bit of a muscle problem here'," Hargreaves said.
"I was surprised it didn't go in the warm-up. I wasn't going to sprint, which sounds comical. I was just going to try to get through 45 minutes because that would have been a start."
