After four matches without a win ahead of tonight's west London derby in the Barclays Premier League, Mourinho's methods have been scrutinised, particularly his omission of Mata.
The Spain playmaker, Chelsea's player of the year in each of the last two seasons, his first at the club, has been told to adapt his game to have a future with the Blues.
"It's part of a process with him (Mata)," Mourinho said. "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 is 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.
"I want to build with Oscar as my number 10. 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."
Although he would not elaborate on his reasons for leaving Mata on the periphery, Mourinho's initial thoughts appear clear.
The World Cup winner, who signed a five-year contract when he joined from Valencia in 2011, has made three appearances this term, but was hauled off after 65 minutes against Aston Villa, 57 minutes in last weekend's defeat at Everton and featured for 23 minutes against Basle, who inflicted Chelsea's first home Champions League group stage loss in nearly 10 years.
In World Cup year he is unlikely to be content with being marginalised, a decision which fans and pundits alike have questioned.
"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 Basle, 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."
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 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.
After losses to Everton and Basle in the last two games, Mourinho is determined his 62-match unbeaten run at home in the Premier League does not end against Fulham.
He added: "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."