The 31-year-old playmaker has decided to join the national side in Osaka after tests ruled out any fracture or ligament damage, the Japan Football Association (JFA) told Reuters on Monday.
Nakamura limped out of a J-League game at the weekend after taking a kick to his left foot.
"We look at what extent he can play," Japan coach Takeshi Okada told Japanese media at his team's training camp. "I don't want him to force it and make the injury worse."
"There are one or two players whose condition I am a little worried about. I have an idea about the way I want players to fit into the system but I don't want to push them too hard and have them break down. That would be a serious headache."
Nakamura said he was ready to play against fellow World Cup qualifiers Serbia.
"I'll strap padding on for training but I won't have it strapped for the game," said the Yokohama F-Marinos midfielder. "It's swollen and sore but I think I can cope with it.
"It's important to join up with the Japan team as the World Cup is so close."
Yokohama coach Kazushi Kimura has given Nakamura the green light despite voicing his concerns.
"He's been through a lot with previous World Cups," said Kimura, referring to former Japan coach Philippe Troussier's shock decision to drop Nakamura from his 2002 squad.
"What happened in the past is probably playing its part in his insistence on playing. The ankle is swollen and I have told him to be careful."
Japan, who have never won a game at a World Cup tournament on foreign soil, have been drawn against Cameroon, the Netherlands and Denmark in Group E in South Africa.
The Blue Samurai face World Cup-bound South Korea at home on May 24 before flying to Europe for warm-up matches against England in Austria on May 30 and Ivory Coast in Switzerland on June 4.
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