The 24-year-old was substituted after 35 minutes of Chelsea's 1-0 loss to Manchester City in the Premier League last Saturday with the injury to his left hamstring.
He was ruled out of Spain's World Cup qualifiers with Albania and Israel after an MRI scan showed "a grade II myofascial injury in the hamstring muscles", the Spanish Football Federation said.
Such an injury could result in a month-long absence, but Chelsea hope Morata will be available sooner. He has now reported back to the Blues' Cobham training base for assessment and rehabilitation.
The former Real Madrid and Juventus striker on Tuesday posted a photo of himself in a Chelsea training top, with a target emoji ahead of Crystal Palace, the Blues' next opponents on October 14.
He wrote on Twitter: "I have no time to lose! Working hard towards recovery! Crystal Palace."
Following the City loss, Chelsea head coach Antonio Conte expressed hope Morata's departure had come prior to serious injury.
No timeframe for his recovery has been given after the scan in Madrid and he has now returned to London to work with Chelsea's medical team.
The Blues are six points behind Premier League leaders City and their game at Palace is their first of six in 18 days.
Morata has scored seven goals since signing for £58 million from Real Madrid as a direct replacement for Diego Costa, now at Atletico Madrid.
His possible absence will give Michy Batshuayi an opportunity, if Conte selects the Belgian who has netted five times this season, including the winner at Atletico last week.
Batshuayi was overlooked against City as Willian was sent on as a substitute for Morata, while Conte has also spoken of using Eden Hazard as a 'false' nine.
A month-long absence for Morata could impact Chelsea's Champions League hopes - two of the six games before the end of October are against Roma - but the other matches are more favorable and might be seen as an opportunity to rest Morata anyway.
As well as pointless and scoreless Palace, Chelsea face Watford and Bournemouth in the Premier League, plus Everton in the Carabao Cup fourth round.