Drogba had just put the Ivorians ahead when he was injured in a 15th-minute clash with Japan central defender Tulio and left the field clutching his right arm. Unconfirmed reports from Switzerland suggest the Chelsea star has fractured his elbow.
Coach Sven-Goran Eriksson said: "It's an elbow injury for sure. How bad it is, I don't know. He had a lot of pain.
"Of course I am worried, he's our captain and one of the best players in the world," added former England boss Eriksson, who attached no blame to Tulio. "It was unlucky, he didn't want to hurt anyone. Football is a game of contact."
Drogba was in sparkling form for Chelsea last season, playing a pivotal role as Carlo Ancelotti's men landed the Premier League and FA Cup double. His absence in South Africa would seriously hinder his side's chances of qualifying from Group G, which also contains Brazil, Korea DPR and Portugal.
Côte d'Ivoire won the game 2-0 with Manchester City defender Kolo Toure adding a late second for Les Elephants.