The Sevilla defender filled in at right-back for Les Bleus as they continued their winless run in this season's Nations League campaign following a 1-0 defeat.
Kounde was substituted at half-time and Football.London claimed that the procedure had been "a long time coming," with the problem reportedly dating back "several months."
The 23-year-old is said to have played through injury, with his appearance at the Stade de France his 55th of a grueling season.
Speaking to Foot Mercato, under-fire boss Deschamps claimed:
"I know very well his athletic condition today. Tomorrow, he will have an intervention (surgical) because he has a problem that dates from several months ago."
The defender has been consistently linked with a move to Chelsea this summer. Marca has claimed that Sevilla will not allow Kounde to leave for any less than €65 million, with the Frenchman still having two years left on his current deal.
The Blues are desperate to recruit a top-class centre-back this summer, with Antonio Rudiger and Andreas Christensen both leaving Stamford Bridge on free transfers at the end of June.
Thomas Tuchel aiming for "squad rebuild" at Chelsea this summer
Following the controversial departure of Roman Abramovich, Chelsea are under new ownership, with a consortium led by LA Dodgers owner Todd Boehly taking over.
According to The Mail, the American wants to gift Tuchel "A-list" signings, following a mixed campaign on the pitch in which they won the Club World Cup, but lost both domestic cup finals.
When asked by Football.London what his hopes are for this summer, Tuchel claimed:
"We are rebuilding, not improving the squad. We are rebuilding. This is always challenging, but we are up for the challenge.
"I don't know where we are from day one. What I can promise is that I will be here – if I can promise that – I will be here with full energy and positive energy no matter what. We will still work for Chelsea, and I refuse to think of negative scenarios. We will be competitive, on which level we will see."
The German boss was widely praised for the way he handled an extremely difficult situation towards the end of the season, as the west London club ultimately finished third in the Premier League.