The Real Madrid forward remained at France's training base while the rest of Zidane's squad took part in the session.
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The session was the second overseen by new France coach Zinedine Zidane, who is preparing for his first match in charge when France face Turkey in Kocaeli on Friday.
France are also scheduled to play Belgium home and away and host Italy during the international window.
Mbappe's condition adds an early selection concern for Zidane as he begins his tenure with the national team, after replacing his former France teammate Didier Deschamps following the World Cup.