The Manchester United striker has failed from the spot nine times since arriving at Old Trafford in 2004 - including against Arsenal last weekend.
He has found the target on 16 occasions, but Ferguson feels the England international should have a higher conversion rate if he is to be considered United's go-to man from 12 yards.
Ferguson said: "Wayne will never come to me and ask not to take them, but I can tell you he will not want to miss another one.
"I think that Wayne has to accept that he has to have a better strike-rate with his penalties. He has to produce better - but he is capable of it."
Ferguson, who has also seen Robin van Persie, Nani and Javier Hernandez fail from the spot this season, added: "If you hit the target, you are relying on the keeper to make a great save. If the keeper does so, full marks to him, but you have to give yourself the chance of making sure he has to make a great save.
"The one thing about him (Rooney) is that it wouldn't matter if it was a World Cup final or a first round cup game against an amateur team, he would still want to take them.
"But if he misses another one, then I'm taking them!"