Phil Foden, Cole Palmer, and Ollie Watkins have been ruled out from the England squad for their upcoming Nations League fixtures.
Manchester City forward Foden, recently named PFA Player of the Year, was selected by interim England manager Lee Carsley but will miss the squad due to illness.
Guardiola earlier raised concerns that Foden may need to withdraw from the England squad due to a virus.
“I don’t think so right now,” he said.
“I think he will not go, but I don’t know.
“He doesn’t feel well — otherwise he would be here. But like I said before, national teams decide.”
Guardiola added: “He doesn’t feel good. It’s his stomach, a little, little virus.
“Some people said antibiotics and so on will be fine.”
Chelsea forward Palmer and Aston Villa striker Watkins reported to St George’s Park but have returned to their clubs “to continue their rehabilitation from ongoing issues,” according to the Football Association.
England will face the Republic of Ireland in Dublin on Saturday, September 7, before hosting Finland at Wembley three days later.
These matches will be England’s first since their defeat to Spain in the Euro 2024 final on July 14.
Gareth Southgate resigned shortly thereafter, and under-21s boss Carsley was appointed interim manager on August 9.
For the upcoming Nations League fixtures, Carsley has called up Angel Gomes, Tino Livramento, Morgan Gibbs-White, and Noni Madueke.
Gomes, Livramento, Gibbs-White, and Madueke all featured under Carsley during his tenure as England Under-21 manager.
Manchester City playmaker Jack Grealish, who was omitted from England’s preliminary Euro 2024 squad, has been recalled, along with Manchester United defender Harry Maguire.
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