Militao was due to take part in Brazil's 2026 World Cup qualification fixtures against Ecuador and Paraguay on September 6 and September 10 respectively.
However, it has been revealed that the 26-year-old will head back to club team Real Madrid, with the Spanish giants then assessing the full extent of the damage.
"On Thursday, the CBF medical department carried out a clinical examination and an MRI on the athlete, which detected a small muscle injury in the right thigh," read a medical statement from Brazil.
"The athlete was withdrawn from the two matches of the Brazilian National Team in the Qualifiers. The CBF expresses its solidarity with the athlete at this time and wishes him a speedy recovery."
How long will Militao be missing for Real Madrid?
According to Relevo, Militao could be on the sidelines for the next two to three weeks with the problem, meaning that he would not be available until the end of this month.
Los Blancos will be back in action against Real Sociedad on September 14, while they will also tackle Stuttgart, Espanyol, Alaves and Atletico Madrid before the end of the month.
Real Madrid will need to conduct their own tests before a recovery timeframe is set, but Militao is almost certain to miss at least a couple of matches for the European and Spanish champions.
Aurelien Tchouameni and Ferland Mendy have also been forced to pull out of the France squad during the current international break, although the pair are both expected to be fit for the game at Real Sociedad.
Tchouameni could be required in the middle of the defence alongside Antonio Rudiger in the next match, as David Alaba remains on the sidelines due to a serious knee injury.