Ferdinand's early season appearances have been limited because of a thigh injury he picked up on international duty with England last month.
"It is a concern for us and something we could have done without," said Ferguson.
The £29.1million defender missed United's opening four games, plus the World Cup win over Croatia that sealed the Three Lions' place in South Africa next year.
Ferdinand's injury problems date back to last December, when he suffered back spasms during the Club World Cup that kept him out for six weeks.
The former West Ham skipper then nearly missed the Champions League final with a calf injury he suffered in the semi-final win over Arsenal.
It means Ferdinand missed nine Premier League games in succession up to last weekend, plus four England internationals out of the last five. However, when he returned at Tottenham last week, it appeared his worries were over.
Instead, Ferdinand was immediately consigned to the stands once more in Istanbul during the week after reporting some discomfort in training on Monday. And now he is a doubt for Sunday's eagerly-awaited clash with Manchester City.
"He has one game back and picks up another injury when he really needs some games to get back to his maximum," added Ferguson.
"We don't need to make a decision right away but he really has to do something positive in training to give himself a chance. We hope he is there though. We want all our big players for this particular game."