The Belgian Football Association revealed that the influential central defender was taken to hospital on Wednesday and is awaiting to discover the extent of his injury.
"No @vincentkompany at training today. He was taken to the hospital for a calf scan. We'll have to wait for the results," read a Tweet from the Belgian FA.
Kompany was due to feature for his country in a friendly against Australia in Liege on Thursday.
The 28-year-old has featured in all three of Manchester City's Premier League matches this season after signing a new long-term contract with the Premier League champions last month.
City boss Manuel Pellegrini will be hoping Kompany is not facing a lengthy spell on the sidelines, with Arsenal, Bayern Munich and Chelsea their next three opponents.
