The Manchester City defender is facing a fight for his future at the club, with Kalidou Koulibaly among the centre-backs Guardiola is considering a move for in the summer.
Stones has been on the fringes this season and has failed realise his potential following a £47.5million move from Everton in 2016.
A return to his former club is believed to be one of his options as he plans his next move.
Guardiola has been a fierce supporter of Stones and made him a priority target when first taking over at the Etihad four years ago.
But injuries and inconsistent form have hindered his development, with Guardiola accepting he must go into the market to bring in a top-class replacement for Vincent Kompany, who walked away from the club last summer.
The City manager claimed in 2018 that Stones’ position was secure for the long-term, saying: “I don’t know how long I will be here in Manchester, but as long as I’m here, John Stones will be with us.”
But discussing the 26-year-old’s future ahead of Wednesday’s game against Newcastle, he was less certain.
“I’ve said many times I’m more than delighted with John as a person, as a professional, everything,” said Guardiola. “What I want is the best for him. We’ll speak at the end of the season about what is going to happen.
“Sometimes my wish is not the wish of the players, or the wish of the situation for the club. At the moment I will feel it, if we have to change, we’ll talk to them.
“He’s a young player and we want him to be consistent, to train and recover. There are players who can play every three days for 11 months, others struggle more to be fit and we try to find the key to playing every three days. This is what we want.”
Stones hasn’t started a Premier League game since January 18 and has seen converted midfielder Fernandinho and 19-year-old Eric Garcia overtake him in the pecking order.
It follows long periods out of the team in each of his four seasons at the club after failing to establish himself as a guaranteed starter in the heart of defence.
Now Guardiola has revealed his frustration over the England international’s injury record.
He said: “It’s difficult for a player and for all of us. So the quality of John is there, never doubt it for one second. It’s just when you don’t play, you are rotated and injured again. And injured again.
“They are good when they play in a routine, they are confident. You need minutes, playing being fit or injured and this is what happened with John.
“We have Eric, Nico (Otamendi), Aymer (Laporte), Fernandinho. Eric is doing incredibly well. He must play for himself and focus.”
Stones is set to start against Newcastle, with Guardiola adding: “Of course, what we want for his future and for ours, is for him to come back and play and to be able to play two, three four months with no injuries.”