Van Nistelrooy will definitely miss next Wednesday's Champions League tie with Olympiakos in Athens, although Nicky Butt could return after his ankle injury.
"Ruud won't play against Olympiakos on Wednesday, although hopefully Nicky Butt will," Ferguson told MUTV.
"We are going to try to sort it out once and for all. When you play with a tight hamstring, it's not easy. We want to solve the problem and get him back playing again all the time."