Portugal have one win and one defeat in their first two Group F games and have a huge clash with France coming up on Wednesday.
Mourinho hasn't been impressed with Fernandes' performances so far, with Mourinho expecting more after a strong domestic season at Manchester United.
The soon-to-be Roma manager said per The Sun: "Portugal at its highest level can beat anyone.
"But we need to play with 11 players, in these two matches Bruno Fernandes was on the pitch but not playing.
"I hope he turns up against France, because he's a player with incredible potential.
"He can pass, he can score. He can get penalties, he can score penalties, he can score free-kicks.
"He has a lot to give, but the reality is in these two matches he was not there."
Cristiano Ronaldo has scored three goals in the competition while Bernardo Silva and Diogo Jota have impressed.
Mourinho is keen for Fernandes to start performing alongside the three "fantastic" forwards.
"Portugal has three fantastic attacking players, Bernardo Silva, Cristiano [Ronaldo] and [Diogo] Jota.
"We need that connection, but until now Bruno is not playing."
ITV pundit Graeme Souness has also pinpointed the 26-year-old's body language as a potential issue.
Per Liverpool Echo he explained: "[Fernandes is] an exceptionally talented boy, there is so much to like about him. A great striker of the ball, when he shoots he makes the goalkeeper work.
"I played with players that would not be accepting of the thing you just touched on [petulance], you know he doesn't get the ball and he is waving his hands around.
"He would not have lasted more than five minutes in my dressing room, but he is a wonderful talented boy."
Souness continued: "It would be more along the lines of 'Who do you think you are? We play as a team, we win together, we lose together.'
"Sometimes you will make a bad pass, sometimes you will not see the whole picture
"So all that nonsense, shaking your head and waving your arms at your own teammates, is a no no for me."
Portugal won their opening game 3-0 against Hungary then slipped to a 4-2 defeat against Germany on Saturday evening.
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