Defender Kolo Toure said Drogba had told his team mates that his World Cup was over although coach Sven-Goran Eriksson said he was still hopeful he could play.
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Drogba, 32, a talismanic figure for the Elephants with 42 goals in 67 appearances, limped off after a crunching challenge from Tulio sent him falling awkwardly to the ground after 15 minutes (see video below).
He was taken to hospital and a team source said that he had fractured his elbow, although there was no official confirmation from Ivorian officials.
His absence would be a huge blow to the Ivorians, who have been transformed from a middle-ranking team to a major force in African football since Drogba came onto the scene.
STILL A CHANCE
"It's obviously very sad, for him he said that the World Cup is finished, we're just waiting for what the doctor says," vice-captain Toure told reporters.
Eriksson said, though, there was still a chance Drogba could play at the tournament which kicks off next Friday.
"We are not sure yet, we think it's still a possibility," he said amid chaotic scenes in front of the ramshackle Tourbillon stadium.
Drogba left the stadium with his arm in a cast and a wry smile on his face as he walked to the team bus amid heavy security, cheered by around 50 onlookers.
Ivory Coast won the game, only their second under Eriksson's leadership, 2-0.
Drogba set up the first goal when his free kick was deflected into the net by Brazilian-born Tulio for an own goal. Toure sidefooted home the second goal nine minutes from time to condemn Japan to their fourth successive defeat.
"It's difficult for us to lose such a really important player," said Toure. "I think the news is not the best, maybe he will even not play the World Cup and it's really bad for us.
"We are just waiting for the doctor to take the decision because we don't know yet.
"He's such an important player, he's a really important player even if he's not on the pitch, to have him with us, it would be really nice to have us by our side, we hope he will come back.
"He was sad and that's it. We can just see that he was sad and when you say that, you can't ask any more."
Born in Ivory Coast and raised in France, the Chelsea forward has helped them qualify for their first two World Cups in 2006 and 2010, the first at the expense of Cameroon.
He was the Premier League topscorer this season as Chelsea won the title from Manchester United.
Ivory Coast have been criticised as being over-dependant on Drogba but Koure said his
