Mikel, 29, captained his country to bronze in Brazil this summer but has not played for the Blues this season.
Rohr said: "There is a reason why Mikel is not playing for Chelsea right now and that reason is because he played for Nigeria at the Olympics."
Mikel will play in Saturday's World Cup qualifier against Algeria.
The Super Eagles, who failed to qualify for the 2017 Africa Cup of Nations, have set the pace in Group B, winning their opening game against Zambia while Algeria could only draw with Cameroon.
Rohr added:  "I cannot punish a player who loves his country and shows that he loves the green jersey.
"He is here with us and he is fit and I hope he can play for 90 minutes against Algeria but if it is not possible, we shall see."
Chelsea declined to comment on Rohr's statement, but when asked about Mikel last week, Chelsea manager Antonio Conte said: "Mikel is working very well now.
"In the past he's sometimes had some injuries. But now he's working very hard, and I'm pleased with his work-rate."
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Chelsea are punishing midfielder John Mikel Obi for representing Nigeria at the Rio Olympics, says the country's coach Gernot Rohr.