The Daily Mail says Mourinho criticised the midfielder in front of his teammates after he was substituted just 29 minutes into their 2-0 victory over Brondby in Copenhagen on Tuesday.
It was the second time in four days that Mikel's performance had come under scrutiny and his place in the team is in jeopardy after Mourinho's patience finally snapped.
Mourinho was left distinctly unimpressed with his performance in the 2-0 defeat at Rangers last Saturday but he was given another chance in Denmark.
The midfielder did not take it and Mourinho is considering other options as he prepares for tomorrow's Community Shield clash with Manchester United.
The Nigerian was fined by Mourinho last season when he overslept and missed training sessions but he is still highly thought of by his team-mates.
Many of them believe he has the talent to be a top-class player but his failure to carry out Mourinho's explicit instructions is having a negative impact with the management.