Alli was substituted at half-time of Tottenham’s defeat against Everton last weekend and was missing from the squad for their Europa League qualifier against Lokomotiv Plovdiv on Thursday.
The England international was expected to return against Southampton, but Tottenham manager Mourinho did not include him in the matchday squad.
Alli has endured a difficult period over the last two years, with his form dipping badly.
Mourinho was seen accusing him of being “lazy” in training during the All or Nothing documentary that captured life behind the scenes at Tottenham last season.
Alli was linked with a move to Real Madrid as part of the deal that eventually saw Gareth Bale join Tottenham on loan on Saturday, while Manchester United are reported to be interested in the 24-year-old.
Asked if Alli had been left out for fitness reasons, Mourinho’s response suggested there was no guarantee he would get back in the team any time soon.
“No. We have a huge squad, a squad with numbers that are very difficult to manage,” Mourinho told BT Sport.
“I never had it, I don’t like to have it and it’s not easy for me. I start with Son, with Lucas and with Harry Kane and on the bench I still have Moussa Sissoko, Erik Lamela and Steven Bergwijn.
“We have too many players for some positions and some of them are paying the price for this.”
