The 29-year old has a thigh injury which has forced him out of the Blue Samurai's trip to Port Elizabeth for Sunday's friendly clash with next year's World Cup hosts and an Asian Cup qualifier four days later.
"The thigh has been sore for a little while and the same area now hurts even more. There is no way I can go on national duty," said Nakamura according to Kyodo News Agency.
National team coach Takeshi Okada said that Catania striker Takayuki Morimoto may also miss the fixtures.
"I have been told he has an Achilles tendon problem and there is a strong possibility that he will miss out," said Okada.