He picked up an abductor injury on international duty and has not been seen in a City shirt since then.
Various British media outlets have since run stories indicating that he might be allowed to leave Manchester in the summer.
However the club have now insisted that he remains firmly in their plans, and will be a part of the squad come the beginning of next season.
Stones has made 68 appearances for City since joining for around £48million two years ago.
Guardiola himself is confident the player will return soon and feature in the team. "It's getting better," he said. "So hopefully he can play the last games [of the season] and can reach the World Cup."