The Frenchman triggered a national outcry when he himself dumped Nakamura from Japan's squad for the 2002 World Cup which the country co-hosted with South Korea.
"Stick him on the bench," Troussier told Japanese media on Thursday. "Nakamura's place in the Japan team is safe. He's not competing for his place in the side."
Troussier said this season's J-League player of the year Mitsuo Ogasawara should take Nakamura's place - as he did at the 2002 World Cup when Japan reached the last 16.
"Nakamura needs to fight for his place," insisted Troussier during a visit to Tokyo. "There are experienced players more than able to replace him."
Japan have never won a World Cup finals game on foreign soil and face a difficult assignment in South Africa after drawing the Netherlands, Cameroon and Denmark in Group E.
Coach Takeshi Okada has been criticised for targeting a semi-final finish but Troussier said the Japanese were capable of matching South Korea's run to the last four in 2002.
"I think it's possible," he said. "Okada has put together a team of attacking samurai and deserves support. The problem will be stopping players like (Cameroon striker Samuel) Eto'o."
Troussier added: "The opening game against Cameroon is a match they can't afford to lose. If they do it could be a repeat of (their quick exit at) the 2006 World Cup in Germany."
