The 25-year-old England international has missed 19 of City’s 31 games this season, making just 12 appearances in all competitions.
Stones last featured for the champions in the 2-1 defeat to Manchester United on December 7, when he suffered a thigh injury but is set to make his return in Saturday’s FA Cup tie at home to League Two side Port Vale.
It has been more than a year since the former Everton defender strung together a run of five successive games for Manchester City, and Guardiola reckons his fitness needs to improve if he is to fulfill his potential.
"He has the conditions to do it, but to be the best central defender you have to play one entire season, every three days being there," said the City boss.
"It's difficult to reach the potential that he has, he has to be at the level to play regularly. The last three seasons and a half he could not do it.
"Sometimes when you have a tough injury - for example like Aymeric (Laporte) had this season or (Ilkay) Gundogan in the first, or (Benjamin) Mendy the year he arrived - it's unlucky.
"But in the case of John, I don't know why he has not been able to play regularly.
"We try to help him. We have tried to do the best to help him since the first day of the three-and-a-half years we have been here. We do everything for him.
"It depends on him. It's in his hands and in his head to become one of the best."
