The 28-year-old was also in France's squad for their 2-0 victory over Bolivia in a friendly international in Nantes on Sunday but did not play.
"Unfortunately, N'Golo Kante will not be able to take part in the qualifiers against Turkey and Andorra due to a knee injury," the FFF said on Twitter on Thursday, adding that coach Didier Deschamps would not call up a replacement.
France, who currently top Group H after both their qualifiers so far, play Turkey in Konya on Saturday before facing Andorra three days later.
Albania, Iceland and Moldova are the other teams in the group.
(Reporting by Simon Jennings in Bengaluru)
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