The club's player of the year from last season has found himself dropped this term, with Mourinho preferring to employ Brazilian playmaker Oscar in the number-10 role.
Mata, who will apparently be the subject of January bids from Atletico Madrid and Paris Saint-Germain, was once again an unused substitute as Chelsea lost to Basel in the Champions League on Tuesday night, and his manager has indicated that is not likely to change due to the form of Oscar and Eden Hazard.
Mourinho told the London Evening Standard: "There is one thing that is obvious, which is I can't change the rules and I can't start the match with 12, 13 or 14.
"I'd love that because many people deserve to play and Juan is one who deserves to play because of the way he works, behaves, the way we see him every day. But if I play him and I don't play Hazard or Oscar, you are asking me about Hazard or Oscar in this moment.
"It's a consequence of the squad we have where, for these positions behind the striker, we have so many options. It's hard for me. I don't have a special pleasure leaving players out. I enjoy playing them and making them happy, but there's nothing I can do."
Hazard and Oscar have made 34 Chelsea appearances between them this season, scoring five and six goals respectively, while Mata has only started eight games in all competitions.