The Everton defender, who is on standby in case Phil Jones fails to recover from a shoulder injury in time for the Brazil tournament, twisted his knee in training yesterday, preventing him from taking part in today's session.
The team's manager told reporters: "We had a slightly unfortunate incident yesterday with John Stones. He twisted his knee very slightly in training.
"It's nothing serious and he could have trained today but we chose to leave him out because it is so early on and we don't want to run any risks.
"In training sessions, things are always going to happen, be it a knock or a slight kick. It's so far so good apart from John Stones, but John will train tomorrow."
The squad has been training in Portugal this week.