Spain host Albania in Alicante on 6 October before travelling to Israel three days later - with Julen Lopetegui's side needing four points from their final two games to confirm qualification for Russian Federation 2018.
Spain conducted their own tests on the 24-year-old on Sunday at the Sanitas University hospital of La Moraleja in Madrid, where a scan apparently revealed the myofascial injury.
Many questions were raised when the Blues chose the £70-million Morata to replace the outgoing Diego Costa, considering the fact that the Spanish global had never managed to really establish himself as a first-team regular at Real Madrid.
Dani Carvajal is absent after missing Real Madrid's 2-0 win over Espanyol with a virus while Andres Iniesta also has a hamstring problem and Barcelona say he will be out for 10 days. He said to me: "Coach I prefer to stop, otherwise I risk having a bad injury", the Chelsea boss said in the press conference following the defeat to City.
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Afghan special forces managed to repel the attackers, killing four in an ensuing gunbattle, officials said. It gave no further details. "Such statements are not supported by any evidence", the ministry said.
The injury is not believed to be a serious one and the Chelsea camp are hopeful that Morata will be fit and available to add to his six Premier League goals in two weeks time when they take on Crystal Palace who prop up the table.
The forward was called up by the Spanish national team but has since been replaced in the squad after picking up an injury.
Real Sociedad right-back Alvaro Odriozozla and Las Palmas midfielder Jonathan Viera will fill the voids left by the unavailable pair.