Flutey, who missed England's autumn campaign after undergoing shoulder surgery, suffered the injury during a non-contact training session on yesterday morning.
"Riki took a bang yesterday in training and he is out with a dead leg," said England coach Martin Johnson. "I don't think Riki's injury is too bad. It was touch and go whether he would be fit and we think he isn't going to make it.
"It is a blow because we picked him to play there. The good thing for us is that Toby has played a lot of Test rugby at 12. He has a kicking game and is an experienced Test player now."