Rooney appeared to turn over on his right ankle in the build-up to Bayern Munich's injury-time goal which gave the German side a 2-1 victory in the first leg of their Champions League quarter-final tie.
Rooney has been in consistently destructive form in recent months, and scored his 34th goal of the season inside 64 seconds at the Allianz Arena, so news of a fitness concern is a real worry for United and England.
The striker, who left the stadium on crutches and with a protective boot in place, had to be helped from the pitch after going down in pain and Ferguson is unsure whether Rooney will be fit to play in a critical match against title rivals Chelsea at the weekend.
"He's obviously hurt his ankle," he said. "We'll know better tomorrow. It's too early to say. I don't think it's terribly serious, but we'll wait and see."
Asked if he could feature against Chelsea on Saturday, Ferguson added: "I can't answer that, we need to wait until tomorrow."