"Kaka hasn't played for six months, but it has actually been longer because he hasn't been in optimum form for a year and a half," he told a news conference after morning training.
"He relies on his talent and speed, which doesn't make this situation easy for him. I didn't expect him to be the Ballon d'Or winner he was as soon as he recovered," he added.
The 28-year-old Brazilian underwent surgery on his left knee on 5 August and only returned to training in December.
"He is going through a natural process and we must continue to support him. He is a fantastic guy and a great player. We must be patient and allow him to work with no pressure. I don't put any pressure on him," Mourinho said.
Mourinho has included 20 men on his squad list for Thursday's clash with Malaga at the Bernabeu.
Midfielder Sergio Canales returns after recovering from an ankle sprain. Winger Pedro Leon also makes the cut.
But Portuguese international Pepe is out with flu, along with injured teammates Argentine defender Ezequiel Garay, German midfielder Sami Khedira and Argentine forward Gonzalo Higuain.
"We'll have to win against Malaga and we will have to take risks. Malaga are a good team. They have experienced players and a good coach," Mourinho said.
"I'm practically sure they won't be relegated this year. Having won all our home games does not guarantee we'll win again on Thursday."
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