Morata limped off during the first half of Chelsea’s 1-0 defeat by Manchester City at Stamford Bridge on Saturday but initially travelled to Spain for international duty earlier this week.
However, the 24-year-old withdrew from Julen Lopetegui’s squad on Monday ahead of the upcoming World Cup Qualifiers against Albania and Israel.
The Spanish Football Federation claims the striker has a grade-two hamstring injury, but he returned to Chelsea on Tuesday for further assessment.
Alvaro Morata could be out for six weeks after his hamstring injury was deemed worse than first feared. If confirmed, he is set to miss a number of very important fixtures.
The news comes as a massive blow as originally Chelsea boss Antonio Conte hoped he would be straight back after the international break.
It also leaves Chelsea desperately short of attacking options with Michy Batshuayi their only back up.
If the former Real Madrid striker is out for the entire six weeks then he will miss games in both the Premier League and Champions League.
On October 14th Chelsea travel to Crystal Palace before hosting Roma in Europe just four days later. From there they will take on Watford on the 21st before playing Everton in the Caraboa Cup.
On the 28th of the month Conte’s men travel to Bournemouth, and then three days later jet off to Italy to take on Roma.
The Blues will then host Man United at Stamford Bridge on November 5th – their first game of the month, and the one they will be desperate to have Morata play in.
Following this the south-west London club will have a 13-day break, around the same time Morata will definitely be returning to the first-team, should his recovery go to plan.
Morata has bagged seven goals in nine appearances since a £60million move from Real Madrid in the summer.