Kyle Walker, Andros Townsend, Adam Lallana, Steven Caulker and John Ruddy all underwent recovery work instead of taking part in the session at Tottenham's training ground.
Spurs boss Tim Sherwood suggested full-back Walker would play no part for England after he was sidelined for Sunday's 1-0 win over Cardiff.
"He was not fit to play here today, so he won't be fit for England either," said Sherwood following the match at White Hart Lane.
"I'm not sure but he probably will (link up with England) as they will be training at our complex in the early part of the week."
Lallana played the whole of Southampton's 3-0 defeat to Liverpool on Saturday, but was not deemed fit enough to train with his England team-mates.
Cardiff defender Caulker, Tottenham winger Townsend and Norwich goalkeeper Ruddy were given more recovery time after playing in Premier League fixtures on Sunday.
Southampton's teenage full-back Luke Shaw took part in his first England training session and could make his debut at Wembley.