The Scot, who has not played for United since December, has been suffering with a mysterious bowel illness.
"He has got challenges that we are happy to be patient with. But he won't be starting the season," Ferguson said.
"Darren has not started training with us. It's a shame because he's such a magnificent professional and nice guy."
During his absence, Fletcher has been in a coaching role with the reserves while Fergie said, "If it doesn't work out for him, he knows he has always got a position at this club."
With over 200 appearances for Manchester United, Fletcher has committed himself as a one-club man since making his top-flight debut back in 2002.
Meanwhile, United unveiled two new signings Shinji Kagawa and Nick Powell. However, Ferguson hinted there could be more signings this summer.
"It's possible we could bring one more in, maybe two more," said Ferguson.
"I think we've always done well in terms of getting players at the end of the season," he added.