The 28-year-old, who was fifth in the World Cup last season, is suffering from a vascular problem in the legs.
A statement on the French Ski Federation website said: "The syndrome is caused by trauma, fracture or excessive compression of the lower limbs that prevents the expansion of muscles. It causes severe pain and should be treated urgently, surgically."
FFS indicated that this kind of disease often affects "high level skiers practising intensely by roller skiing".
Fourcade could return in time for the World Championships in Nove Mesto in February.
He won two silvers at this year's World Championships in Ruhpolding, a year that saw his younger brother Martin win three golds plus the Crystal Globe as overall World Cup champion.
The season begins with a mixed relay in Ostersund, Sweden on Sunday but Martin Fourcade will not be in action.
"It's a matter of programming and cumulative fatigue," his coach Stéphane Bouthiaux said.
Fourcade junior will be in action in the 15km individual event the following Wednesday.