Belgian coach Marc Wilmots and the English Premier League club had agreed a preventative approach to the injury that the centre back has been struggling with over the last weeks.
Kompany will be considered for Belgium's last Group B qualifier at home on Tuesday to Israel if fit, federation officials added.
City manager Manuel Pellegrini has criticised Wilmots' decision to name Kompany in his 23-man squad for the two qualifiers, which are expected to confirm Belgium’s participation in next year’s finals.
Pellegrini said he could not prevent Kompany from joining up with the Belgian squad, but made it clear that the player would not be fit to play.
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"Vincent continues to recover from his calf injury and we will see the way he improves the next weeks," Pellegrini said. "But Vincent cannot play (for Belgium).
"I cannot ask him not to travel. If the national team call him, he must go, but he cannot play, so I don’t think he will play."
(Reporting by Mark Gleeson; Editing by Amlan Chakraborty)
