The 29-year-old has yet to feature for the Blues this term and is expected to make way in the New Year when his current deal at Stamford Bridge expires.
Rohr believes that Mikel is not being selected because he chose to represent his country at the Rio Olympics, rather than taking part in pre-season training with Chelsea, but says that he will take a different stance when it comes to picking his own squads.
"Mikel was punished by Chelsea for playing at the Olympics for Nigeria," he is quoted as saying by The Metro. "The new coach tried convincing him to stay but he went to defend his nation. I cannot punish him for not playing in his club."
Mikel himself spoke out on his future this week, backtracking on recent claims that he is willing to fight for his place in the Blues' first-team fold by suggesting his time in West London may well now be up.
"We will wait and see what happens in January," he told ESPN. "For the first time in my career, this is happening to me and I have to stand up and deal with it.
"It is what it is but I'm training hard every day and I always wish the team the best and I am happy we are doing well. I've been at Chelsea a long time. Managers come and go, players come and go. I've been at Chelsea a long time and these things happen in football. So we will have to make that decision when January comes."
Mikel is Chelsea's second-longest serving player behind John Terry, winning 10 major trophies during his time at the club - including two Premier League titles and the Champions League.