Kante has started every Premier League match for Chelsea this season and the 29-year-old played the full 90 minutes of France’s goalless draw with Portugal last weekend.
But Didier Deschamps left Kante out of his 23-man squad to face Croatia – a repeat of the 2018 World Cup final – with Rennes’ Steven Nzonzi coming into France’s starting XI in Zagreb on Wednesday evening.
Antoine Griezmann and Kylian Mbappe scored either side of Nikola Vlasic’s stunning 64th-minute strike to seal a 2-1 victory for the visitors.
According to L’Equipe, Kante appeared to train as normal on Tuesday but has been suffering with muscle discomfort which ruled him out of the game.
Kante would have been in line to make his fifth start of the Premier League campaign at home to Southampton this weekend.
Chelsea will also be assessing the fitness of summer signings Ben Chilwell and Edouard Mendy over the next couple of days.
Chilwell recovered from an illness but had to withdraw from England’s training camp earlier this week with a pre-existing foot injury.
Mendy has been struggling with a thigh issue but is hopeful of being able to feature against Southampton.
There was some good news for Chelsea this week, though, as Hakim Ziyech and Christian Pulisic were pictured in training on Wednesday.
Ziyech, who signed from Ajax for a fee of £33m in the summer, sustained a knee problem in pre-season and could make his Premier League debut versus the Saints at Stamford Bridge.
‘It felt great (return against Crystal Palace). I had another tough injury, and it was really hard work to get back out there,’ the American told CBS Sports when asked about his fitness earlier this week.
‘I’m really excited I got some minutes before the break.
‘Now I just wish we had a game sooner, to be honest. ‘But at least I’ll get a little rest.’