Chilwell grabbed the back of his left thigh after making a sprint, falling to the ground before being helped from the field by Chelsea's medical staff.
"It doesn't look positive, but it's a hamstring. We'll have to scan it and see what it is," Chelsea manager Graham Potter told broadcaster BT Sport.
Former England boss Glenn Hoddle, who guided the team at the 1998 World Cup in France, said that he doubted Chilwell would recover in time.
"I feel for him dreadfully ... that one just went. His face went and as he touches the ball he grimaces and looks in real pain. It looks like a nasty one," he said.
Chilwell's Chelsea team mate Reece James has been ruled out of the Qatar tournament after suffering a knee injury, and Manchester City right back Kyle Walker is struggling with a groin problem.
The final FIFA deadline for World Cup squads is November 13th, a week before the tournament kicks off on November 20th.
