The incident, the latest in a series of issues between the two, was first reported by French television. Sources told ESPN that the row erupted during a training session on Monday and then continued in Mourinho's office at the Tottenham training ground in Enfield, north London.
Ndombele, 23, who joined Spurs last summer from Lyon for €62 million -- the most expensive player in the club's history and one of the highest earners with a salary of just under £10m a year -- has had enough of the constant criticism and taunts coming from his manager, either in private or publicly, which have happened since Mourinho replaced Mauricio Pochettino last November.
Ndombele felt he was set for a new start under Mourinho, having followed his requests during the United Kingdom's coronavirus lockdown. He lost weight, and even responded positively to Mourinho's request to undergo a training session in a park in north London, despite the fact this contravened government guidelines. Mourinho later apologised for the breach.
However, since the team went back to training, Mourinho told the France international that he was still not ready to start and that he was not doing enough during sessions. However, Ndombele believes he is at 100% of his capacity, yet he stayed on the bench in Spurs' two games since the restart, against Manchester United and West Ham.
Ndombele's agents Romain Fernandez and Mounir Sidhoum are now looking for a resolution, though clear-the-air talks between the pair appear unlikely. Sources have told ESPN there is no way back at present, at least on Ndombele's side.
The other option is a move away. Pini Zahavi, the agent who brokered Ndombele's move to Tottenham, will be heavily involved again if a transfer is arranged. Last summer, after being convinced by Pochettino, Ndombele chose Tottenham ahead of Juventus, Paris Saint-Germain and Barcelona.
PSG are still keen on the player but are not ready to spend €60m-70m on him right now. However, they could be tempted by another structure like a loan with option to buy, sources have told ESPN. PSG's sporting director Leonardo is very close to Zahavi.
It is the same for Barcelona who do not have the money right now for such a deal. But a loan could work for them as well as a swap, despite those deals being difficult to make.
Bayern Munich, who could lose Thiago Alcantara and are looking to sell Corentin Tolisso, could also come in for Ndombele. They have the money and the possibility of a swap deal involving Tolisso, plus cash, could be an option, sources have told ESPN.
Tottenham's next game away at Sheffield United on July 2.