Morata, who has had an electric start to his Chelsea career, was forced off after just 35 minutes during the 1-0 defeat to Manchester City at Stamford Bridge.
The 24-year-old was withdrawn from Spain's World Cup squad ahead of their qualifiers against Albania and Israel during the international break because of the hamstring problem.
The Spanish FA confirmed that an MRI scan showed the striker had suffered a grade 2 myofascial injury in the hamstring.
According to 'Sky Sports', this could leave Chelsea's record signing out for the whole of October, being able to return to first-team action midway through November.
This would mean Belgian forward Michy Batshuayi is the only recognised striker at Stamford Bridge during Morata's absence, after the club agreed a deal to sell Diego Costa to Atletico Madrid in September.
Following the international break, Chelsea face four Premier League fixtures, away at Crystal Palace, before hosting Watford and Manchester United, with a trip to Bournemouth in between.
Morata, who has scored seven goals in his first 10 Chelsea appearances, will be a big miss for the Premier League champions, and is almost certainly going to be absent this month's back-to-back Champions League games against Italian side Roma.