The Spurs boss has been robbed of a number of key players through injury and says the job is getting harder and harder as he attempts to build a winning side.
Mourinho said he is "playing a game of chess without any pieces" after his side overcame selection issues to beat Southampton 3-2 in their FA Cup fourth round replay on Wednesday night.
Spurs produced a late escape as goals in the final 12 minutes from Lucas Moura and Son Heung-min set up a fifth-round meeting with Norwich, but Mourinho admitted the best team lost.
Tottenham went ahead through Jack Stephens' own goal but were heading out after Shane Long and Danny Ings put Southampton in front.
Mourinho was without the injured Harry Kane, Moussa Sissoko, Ben Davies, Giovani Lo Celso and Erik Lamela, while a half-fit Dele Alli came off the bench and Steven Bergwijn was ineligible.
"I cannot speak about the progress I want to make because I don't have the players I want," Mourinho said.
"And the team needs players to progress, collectively, tactically and dynamically. We need to have the players but we don't have the players."
Despite being short on numbers, Mourinho says he cannot fault the attitude and spirit of the players who were out there on the pitch.
Even so, Mourinho is sure to be pushing for a number of quality additions over the summer if he is to have a chance of taking Spurs on to the next level.
There was a sad moment during the second half as Jan Vertonghen, a player who has given eight years of service to Spurs, looked inconsolable having been substituted.
The 32-year-old, who is out of contract in the summer, has been exposed on a number of occasions this season and had the look of a man who knows his days at Spurs are numbered.
Mourinho said: "No injury, it was my decision. It's normal that he's sad. No player likes to come out. I decided to sacrifice Jan, so sad yes and with a reason to be sad, but happy now because he won."