With the north Londoners set to play for a second time in just three days on Saturday, at Norwich, Mourinho revealed the club’s £65million midfielder asked not to be in the squad with concerns about his fitness.
The Spurs boss said: “On Wednesday he told me that he was not feeling in conditions to play the game.
“Not based on injury but based on fears of the previous injuries that he has had since the beginning of the season.
“So, two or three or four injuries and feeling not ready to start the game. But I cannot say that he is injured. I can only that he is not in conditions to play.”
France international Ndombele, who has recovered from a recent groin injury, was a shock omission as Spurs came from behind to beat Brighton 2-1.
Adam Webster put the Seagulls ahead before goals from Harry Kane and Dele Alli extended Spurs’ unbeaten record on 26 December to 14 games.
But Ndombele’s absence was the big talking point and the Portuguese – who revealed the former Lyon man would be taking part in the warm down – was happy to clear the situation up.
“I cannot say he is injured,” said Mourinho. “In five minutes we start a training session and you can go to the stands and watch it, he is going to be training normally so I cannot say he is injured.”