It is a rather sobering statistic given new-boy Robin van Persie has 12 goals and Javier Hernandez has moved on to nine, despite eight of his 17 appearances this term coming from the bench.
Rooney's sharp-shooting has been affected by two fitness problems -- a gashed thigh and a bout of tonsillitis -- that kept him out of six matches in total.
In addition, he has operated from deeper positions following the arrival of Van Persie.
Nevertheless, for a player of Rooney's standing, three is a low figure and Ferguson wants it to improve.
"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."
The midfield idea is something Ferguson has tinkered with before and at times it has worked, especially when United have used the diamond formation.
"I am happy with that part of his game," said Ferguson.
"If he can contribute to the team's success, fine. But we would rather he scored more obviously."
Getting an orthodox striking berth back will be tricky though.
In 2009-10, Rooney scored 34 as a lone front-man, but since the arrival of Van Persie from Arsenal last summer, there has been no disputing who the number one forward is.
"Without doubt Robin is an up-front player," said Ferguson.
"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."
Van Persie and Rooney may operate in tandem at the Madejski Stadium this evening when United visit Reading.
Victory would confirm their status as Premier League leaders ahead of the first Manchester derby of the season at the Etihad Stadium on December 8.
Some critics cannot quite believe United have a seven-point advantage over third-placed Chelsea given that their performances, at times, have been quite poor.
Even midfielder Michael Carrick described Wednesday's win over West Ham as "far from a classic", but Ferguson is not joining the criticism.
"I don't think the form has been that bad to be honest," he said.
"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."
Since losing out to Manchester City on goal difference last season, Ferguson has seemed almost obsessed by the need to improve United's scoring record.
Yet he now concedes it is the strength of his side's defence that could be the major factor.
"Good defenders win you leagues," he said. "There is no question about that."
To that end, news of Nemanja Vidic's imminent return from knee surgery is a major plus.
And, whilst Anders Lindegaard is set to continue in goal for the fourth game running despite David de Gea's recovery from having his wisdom teeth removed, Ferguson accepts constant switching of goalkeepers is hardly ideal.
"I am not happy to rotate all the time," said Ferguson. "I don't think that creates consistency.
"David got an infection, he had two teeth out and his jaw was quite badly swollen so we gave him some time off.
"But Anders has come in and done well and it is one of those situations where there is no actual reason to leave Anders out.
"Hopefully David understands that because there is no long term issue."