Mata, Chelsea's player of the year in each of his previous two seasons at Stamford Bridge since his move from Valencia, has made one appearance this term and was substituted against Aston Villa.
A player so integral to the 2012 Champions League and 2013 Europa League successes, was omitted from Monday's team to play Manchester United and 24 hours later his father and agent was reported to be in the directors' box at Arsenal.
"It was my option (choice)," said Mourinho, who was speaking in Prague ahead of Friday's European Super Cup clash with Bayern Munich.
"He didn't play against Man United, it was my option. I have always reason for the options. I feel that it's my duty to explain to the players the reasons for my options - and I do.
"I don't feel it's my duty to explain to the media the reason for my options. I don't always do (it). Everything is clear between me and the player. We have no problems.
"I think he's a very important player for us. He wants to be a very important player for us. He wants to stay. I want him to stay, the club want him to stay. There is no story."
Mourinho has a host of options in the three players who play behind the main striker, boosted this week with the signing of Willian from Anzhi Makhachkala.
Another player from the Russian club has been linked with a move to west London, but Mourinho would not confirm Chelsea's reported interest in Samuel Eto'o, who played under him at Inter Milan.
A deal for the Cameroon striker has implications for Chelsea's pursuit of Manchester United striker Wayne Rooney.