The striker limped out of Saturday's 1-0 defeat to Manchester City at Stamford Bridge with a hamstring injury.
Morata duly joined up with the Spain squad in Madrid to be checked by medics ahead of their World Cup Qualifiers against Albania on Friday and Israel next Monday.
And the Spanish Football Federation has revealed that the 24-year-old has sustained a grade two hamstring tear.
Morata has now withdrawn from the Spain squad and the injury is likely to sideline him for around six weeks.
That will come as a big blow to Chelsea boss Antonio Conte.