Boro said that the Egyptian, who spent half of last season on loan at Wigan, was absent from the first training at Rockliffe Park on Monday without permission.
Consequently, Boro coach Gareth Southgate has decided to take action against Mido, along with fellow striker Afonso Alves.
"Both players have been spoken to and disciplinary matters have been dealt with internally," Southgate told Middlesbrough's official site.
"Both are under no illusions over what's expected of them in the future. I don't want to say anything else about it."
Furthermore, Boro stated that Brazilian forward Alves has joined his teammates on Wednesday, whereas Mido has yet to appear at Teesside.
Mido's Egyptian mate Mohamed Shawky missed the opening training this week as well, but he was given permission to arrive late from international duty.
Shawky played for 40 minutes in Egypt's 3-0 World Cup qualifying win over Rwanda on Sunday, before being forced out due to injury.