Ford, 31, started at fly-half throughout this year's Six Nations but, having completed the club season with Sale, it has been decided he needs time to recover from the pre-existing condition.
"Naturally we're disappointed that George won't be with us in Japan and New Zealand, but, following specialist medical advice, and in consultation with George himself, we have decided this is the best course of action," said England head coach Steve Borthwick.
"George is a big part of the England team and is an excellent professional who I know will rehab diligently to ensure he gets himself right as soon as he can."
England face Japan in Tokyo on June 22nd before heading to New Zealand to play two Tests against the All Blacks.