Gareth Southgate included the Arsenal winger in a 26-man squad last week but he missed Sunday's 1-0 win against Manchester City after struggling with a hamstring issue during recent matches.
"The forward reported to St George's Park on Monday alongside the rest of the Three Lions' squad," the FA said in a statement.
"Having missed Arsenal's Premier League win against Manchester City on Sunday through injury, Saka was assessed by the England medical team and it was decided that the player would continue his rehabilitation at his club.
"No replacements are planned, with Gareth Southgate having a squad of 25 players to work with."
England host Australia in a friendly at Wembley on Friday before facing Italy at the same venue in a Euro 2024 qualifier on October 17.