Hargreaves was forced to return to the United States for more rehabilitation work with Dr Richard Steadman to try and combat a long-standing tendinitis problem that has kept the England star out of action for almost two years.
Although the 29-year-old did manage a very brief comeback, lasting one half of a reserve game and one minute of a first team appearance as substitute at Sunderland, prompting suggestions of a call to Fabio Capello's World Cup squad, it eventually became apparent all was not going smoothly.
It is widely assumed if Hargreaves does not win this particular battle, his playing career will be over.
"Owen is due back within the next two weeks," said the United boss.
"He seems to be making decent progress now. But if he comes back in two weeks when is he going to be fit to play for Manchester United? That is still to be found out."
Ferguson was optimistic enough to name the former Bayern Munich star in his 25-man Premier League squad but then omitted him from the Champions League squad for the opening group phase.
The Old Trafford chief revealed the differing criteria for domestic and European matches made his mind up about making Hargreaves available for the Champions League, although he can make changes in January should the circumstances require.
"It would be silly to put him in the squad when he is not even back here," he said.
"Quite simply I could not put him in ahead of someone else but I can make a change in January if he is back to his fitness."