Mourinho has admitted that the France international has had a tough time under him due to injuries.
However, the former Chelsea and Manchester United boss has said that he hopes that the 23-year-old improves from now and does not get injured.
Mourinho told Football.London when asked about Ndombele's injury problems: "I can only speak about three months and three months of small injuries, setbacks, difficult to reach a good physical level. Playing one match and then getting injured again. So difficult, difficult time."
The Portuguese added: "At least he's not been injured in the last few weeks, he played a good 30 minutes in the last game and it was a game of high intensity. And hopefully he'll only improve.
"I hope that the first time he plays a match in the starting line-up, he can play and be on the pitch for 60-90 minutes and not have any setback."
Ndombele joined Tottenham from French club Lyon in the summer of 2019.
The Frenchman arrived at Tottenham Hotspur Stadium with a strong reputation, but the youngster has had injury problems and has not made a massive impact for Spurs.
According to WhoScored, the 23-year-old has made 10 starts and six substitute appearances in the Premier League for the North London outfit so far this season, scoring two goals and providing two assists in the process.
The midfielder has also made four starts and two substitute appearances in the Champions League for Tottenham this campaign, providing two assists in the process, according to WhoScored.
Tottenham will return to action on Saturday afternoon when they take on Chelsea away from home at Stamford Bridge in London in the Premier League.
Have something to tell us about this article?