The Spanish striker was subbed off in just the 11th minute of Chelsea's 4-0 Champions League win over Steaua Bucharest on Tuesday night and will now have his problem assessed.
Mourinho was holding hope that it was not a severe injury like that sustained by summer signing Marco van Ginkel recently.
"We have to wait for tomorrow for a scan," he told Sky Sports. "I hope it is not dramatic like van Ginkel.
"I thought it was an ankle injury when he slid in. Hopefully it is not so dramatic."
Mourinho added: "He knows that he doesn't play against Norwich (on the weekend). He knows that he cannot go to the (Spain) national team (for World Cup qualifiers).
"He knows he has 15 days until the next match he can play, which is against Cardiff. Let's see the scan. If the injury is an injury for 15 days, I think he'll be fine. That's okay.
"The problem is if it's more time and it's a pity for the guy, because he's in a very good moment. He played fantastic against Tottenham.
"Today he started the game because he deserved to start the game. It's a pity, but that's football."
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