The England forward has a measly haul of three goals this season, while team-mates Robin van Persie (12) and Javier Hernandez (nine) have taken the limelight.
It has been a frustrating few months for the 27-year-old, with a gashed thigh and tonsillitis keeping him out, as well as playing in a deeper role to accommodate United's wealth of attacking options.
"Wayne is going through a period like all strikers do, he is not scoring," said Ferguson.
"He has missed bits of games and been off with tonsillitis, and Wayne is the type of player who can't miss games because of the frame he has got."
Regarding the use of Rooney within the diamond formation, Ferguson added: "I am happy with that part of his game.
"If he can contribute to the team's success, fine. But we would rather he scored more obviously."
Since the arrival of Van Persie from Arsenal in the summer, Rooney, who scored 34 in the 2009/10 season as a lone front-man, has taken somewhat of a backseat.
Ferguson is delighted with the impact the Dutchman has made and said: "Without doubt Robin is an up-front player.
"He has experience and now our players are starting to realise how good he is. We are getting more aware of the runs he is making and the movement he has up front. Hopefully that understanding gets better."
The Premier League leaders head to Reading on Saturday and although their recent performances have not been attacking classics, including a narrow 1-0 victory over West Ham, their manager is not concerned.
"I don't think the form has been that bad to be honest," the Scot added.
"But when you are manager of this club, you have to go through that analysis about Manchester United not being as good as they used to be.
"We are still top of the league so we must be doing something right."