Fans and pundits alike have been bemused by the way in which Mourinho has used the Spaniard this year, especially as he has been Chelsea's player of the year in each of the last two seasons.
He has made three appearances this term but was hauled off after 65 minutes against Aston Villa, 57 minutes into the loss against Everton and featured for 23 minutes in the surprise Champions League defeat to Basel.
Mourinho insisted throughout the summer he did not want to sell Mata despite media reports, but the former Valencia man is unlikely to be happy with being marginalised in a World Cup year.
Mourinho would not elaborate on his reasons for leaving Mata on the periphery, but was critical of his midweek display against Basel, who inflicted Chelsea's first home Champions League group stage loss in nearly 10 years.
"There are things I cannot speak with you about," Mourinho said.
"But he played against Everton from the beginning and you can analyse his performance.
"And he played against Basel, not like (Demba) Ba or (John Obi) Mikel, coming in to rescue the game, but he came on when the team was winning 1-0 and when he had specific tasks to do.
"It's part of a process with him. One thing is to play with Ramires and Oscar in the side, them closing (down) each side, and Mata as a number 10 behind a striker, to have clever assists and to have clever passes; fantastic actions because he has great talent.
"Another thing to adapt to the way we want to play. In this moment, Oscar is my number 10 and, if somebody tells me that Oscar is not Chelsea's best player since the beginning of the season, I'd have to disagree."
It is up to Mata to prove to Mourinho his willingness to commit to the system which has seen Eden Hazard favoured wide on the left, Oscar behind the striker and others playing on the right - Willian fulfilled the role against Basel.
Mourinho insists Oscar and Mata can play in the same team, but he wants the left-footed Spaniard to occupy a wide right role and track back in defence.
"I want to build with Oscar as my number 10," Mourinho added.
"I want the other two players, from the side (wings), to adapt to that reality and to learn how to do things that they were not ready to do before."
Hard work is something Mourinho requires of his players and he is leading by example as he seeks to overhaul Chelsea's style of play.
The former Porto, Inter Milan and Real Madrid boss said: "It's a problem I enjoy. I've never worked so hard as I'm doing now. Never.
"I had different situations at the other clubs, but here I work hard every day."
The challenge is balancing the overhaul - a style of play which Mourinho says is not a directive from owner Roman Abramovich, but one the whole Chelsea hierarchy agrees with - with achieving results.
Chelsea enter Saturday's Barclays Premier League west London derby with Fulham winless in four matches.
Mourinho added: "I want results. I'm not trying to protect myself behind the style and the project, and say that I don't care about the results.
"I'm not trying to hide. But the reality is we want to play a certain style.
"We all agree. We had one meeting - not five or 10 or 20 - but one, and we were all convinced this was the way we want to do it.
"The project is beautiful. We had two very ugly results - we don't like, we are not used to them... it's a problem for us."