The Portuguese is unhappy with the way his side are portrayed in the Spanish media, claiming the German anchorman, along with Fabio Coentrao, are victimised deliberately
The Germany international arrived at the Santiago Bernabeu in 2010 after a successful World Cup campaign in South Africa, and has since gone onto become an important part of Los Blancos' first-team plans, forming an effective midfield partnership with Xabi Alonso.
However, Khedira does not receive enough credit in Mourinho's eyes, and feels left-back Fabio Coentrao suffers from the same fate.
"I cannot understand why Khedira and Coentrao are criticised all the time in Spain," he told Spox.
"This is because the media are always looking to write something negative. I currently do not know any other player that is better than Sami in his position."
Mourinho also spoke briefly about the situation of Kaka, who is being lined up for a return to AC Milan, and the trainer admits the midfielder's mental state is not helping matters.
"He is a great professional, but it does not help when your head is not straight," he told Record.
"If he decides to stay, he will help us as he did last year when [Angel] Di Maria and [Mesut] Ozil were injured and he was our No.10.
"But if he decides to leave, we will respect his decision."
Meanwhile, Marca reports that the former Chelsea and Inter boss rejected the chance to sign Santi Cazorla from Villarreal last summer.
The publication claims president Florentino Perez offered the Spain international to Mourinho, but the 49-year-old decided against giving the purchase the green light, as he felt the midfielder was overpriced.
Cazorla eventually joined Malaga for €21 million and helped the Andalucian side to a Champions League place in his debut season, but now appears destined for a move to Arsenal following the club's financial problems.