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The in-form Dutch winger, who came on as a second-half substitute, sustained a calf injury in Bayern's 2-1 defeat by Stuttgart in the Bundesliga.
"Maybe it will turn out not to be that bad but it looks difficult for the United match," Bayern coach Louis van Gaal said.
Robben has produced some impressive displays lately as Bayern bid to win the Bundesliga, Champions League and German Cup.
He scored a memorable extra-time goal to help Bayern to a 1-0 victory over Schalke in the German Cup semi final last week.
Bayern host United in the first leg of the Champions League quarter finals on Tuesday.
The second leg will take place at Old Trafford on April seventh.