German broadcaster ARD and Spain's AS.com are reporting that the Germany international will play no further part in the season due to the injury he sustained in Wednesday night's Copa del Rey final win against Barcelona in Valencia.
Real Madrid have not confirmed the news officially, but Mourinho told the press he was stunned to hear talk that his man was out for the rest of term.
Ever eager to avoid mixed messages from the Spanish and German press, the coach clarified the situation.
"The injury to Khedira is important like any other. It's a limitation for the team and there are players who are hard to replace. It is what it is, bad news, but to say he will not return before the end of the season is absurd," he said.
"He will not play tomorrow or on Wednesday because there is no miracle in medicine, but we hope he is back soon."
Madrid are expected to examine the player on Saturday to further diagnose the problem. Their official website said on Friday that Khedira did not take part in the training session ahead of tomorrow's game at Valencia.