The Bavarians, who had enjoyed a successful run in three competitions following the winter break, are stuck in a rut after their second successive Bundesliga loss, 2-1 to VfB Stuttgart on Saturday.
They could also take on United, 11 years after losing the 1999 Champions League final 2-1 when the English team scored two goals in the dying minutes, without their best player this season.
"Maybe it turns out not to be that bad but it looks difficult for the match against Manchester," Bayern coach Louis van Gaal told reporters.
"It would be extremely bitter if he is missing from such a top game," said Bayern defender Philipp Lahm.
Van Gaal, however, does have playmaker Franck Ribery fit as well as central defender Martin Demichelis, who injured his face in Argentina's friendly against Germany this month.
United have no new injury concerns with top scorer Wayne Rooney and defender Rio Ferdinand likely to be fit after being rested from Saturday's 4-0 victory over Bolton Wanderers, their seventh straight win in all competitions.
"They were just a bit tender," Ferguson told MUTV. "Wayne's got a bruise on his foot. If he'd played and got a whack on it, then he would have been doubtful for Tuesday.
"We've got a big week. We have to use our squad in situations like this. I've no qualms about that at all. They've all done their job well and I'll have Rooney and Ferdinand available for Tuesday."
Ferguson, seeking to lead United to their third Champions League final in a row, will also be delighted with Dimitar Berbatov's form.
