The injury restricted Walcott in training and he has now been sent back to Arsenal to continue his recovery.
Manager Roy Hodgson has opted against naming a replacement player for the fixture in Berne. England fly out to Switzerland on Tuesday afternoon.
An FA statement read: "Arsenal forward Theo Walcott will not travel to Switzerland with the England squad today [Tuesday 14 August].
"Walcott reported with a slightly bruised thigh and was unable to train fully, so has returned to his club as a precaution."
Arsenal midfielder Alex Oxlade-Chamberlain withdrew from the England squad on Monday, complaining of an ankle injury.
He was replaced by Manchester City defender Joleon Lescott as England prepare to face the team that knocked them out of the Euro 2012 quarter-finals on penalties.
City goalkeeper Joe Hart and Chelsea forward Daniel Sturridge have also withdrawn due to injury.