Chelsea signed Batshuayi from Marseille in the summer of 2016 - he scored 19 goals in 53 games for the club before being sent to Dortmund on loan.
After getting frustrated at his lack of playing time at parent club Chelsea due to the arrival of club-record signing Alvaro Morata in the summer, Batshuayi was in danger of missing Roberto Martinez's squad for the quadrennial tournament in Russian Federation.
Scans are believed to have revealed ligament damage to his ankle, meaning he faces a race to regain his fitness before the World Cup in Russian Federation.
Belgium are in Group G and are considered favourites to progress as winners, with the other teams being Tunisia, England and Panama.
There may still be a slim chance of the 24-year-old being available to be part of Belgium's squad for the World Cup starting in June.
"I didn't think it looked like the kind of injury that he would be back from quickly", Stoger said in quotes published on Dortmund's official website. "Hopefully it's not as bad as it looks".
Dortmund is fourth in the last Champions League qualification place with four rounds remaining.