The forward, who has scored 10 goals since his summer move from Real Madrid played the full 90 minutes on Saturday as Chelsea slipped to a 1-0 defeat at London
rivals West Ham.
Morata missed two-and-a-half weeks with a hamstring injury earlier in the season and Conte will once again be without the Spain international for the trip to the John Smith's Stadium.
The Chelsea boss said: "Morata is out. He is a bit tired and he has a problem in his back.
"I think when you play every three days, it is impossible to have a training session and to work on the physical aspects. It's impossible. It's impossible because you have to prepare with the players for a game every three days.
"I think we have to face the reality and will try to do our best. If I stay here to complain it is not the right way. We have to try to do our best.
"For sure it is difficult because to face a game every three days is not simple, especially if your squad is not big, but at the same time, we have to face this situation.
"Some players can be tired, that's normal because some players are playing from this summer and our tours in China and Singapore .
"But I repeat we have to find the best solution. We have to find more rotations.
I'm doing this, we will try and do our best with hunger and desire. We will fight." Conte also confirmed he will still be without
defender David Luiz as he continues his recovery from a knee injury.
Midfielder Danny Drinkwater did train on Monday following a fever and was included in the travelling squad for the match in west Yorkshire.
David Luiz will also miss the match at the John Smith's Stadium
Conte added: "We are facing a team in a good moment of form. In the last game they played a great game against Brighton.
"I don't know which way they have prepared for the game against us. At the same time, we have to try to play our football. We must pay great attention to the counter-attack because they have fast players.
"They are in a good moment of form and we must be very good to be more clinical in this game, because in the recent period we
weren't clinical."