The Egypt international was fined two weeks' wages when he failed to turn up back at the club's Rockliffe Park headquarters with the rest of his team-mates on July 6.
Gareth Southgate: "Mido returned yesterday and has been disciplined by the club.
"He's back with us now, but not yet part of the group as he's now following the programme the other players have gone through over the last 10 days or so.
"He will follow that programme until he's on a level with the others, but that won't happen for a few more days at least because he was late he has to catch-up on everything, including all the fitness testing."