Courtois was called up by Belgium despite the problem but has failed to recover in time.
"Thibaut Courtois has not recovered from his hamstring injury and left the group... Get well soon, Thibaut!" the RBFA said on their official Twitter account.
The RBFA said that Belgium manager Roberto Martinez is yet to decide on Courtois' replacement for the friendly with Liverpool's Simon Mignolet likely to start.
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The Belgian's injury makes him a major doubt for Chelsea's crucial Premier League match against Tottenham Hotspur on April 1 as both teams battle to finish in the top four.
(Reporting by Aditi Prakash in Bengaluru, editing by Pritha Sarkar)
