The former midfielder was known for his set-piece prowess and scored a memorable curling free-kick against Manchester United in the Champions League.
The JFA said Nakamura would join coach Hajime Moriyasu's backroom staff for the World Cup, where Japan have been drawn in Group F with the Netherlands, Tunisia and Sweden.
"I gave a lot of thought to the impact my involvement might have at this crucial stage, with the World Cup finals just around the corner," the 47-year-old said.
"But after receiving a passionate and encouraging message from Moriyasu, I decided to accept."
Nakamura won 98 caps for Japan, scoring 24 goals, and played at the 2006 and 2010 World Cups.
He joined Celtic in 2005 from Italian side Reggina and went on to win three Scottish league titles during his four seasons in Glasgow.
He retired in 2022 and became an assistant coach with Japanese side Yokohama FC.
"I am committed to sharing the same vision as the Japan players as they compete on the world stage, and I will do everything to help them achieve their goals," said Nakamura.