Matsui and his former manager with the Yomiuri Giants, Shigeo Nagashima, received the award, which is bestowed on those who have made significant achievements in their careers and are beloved by the public.
"I played for excellent teams, with excellent teammates, for excellent managers in front of excellent fans," Matsui said. "I did my best to lift up, even a little bit, the game of baseball that is so beloved by the people of Japan."
Late Prime Minister Takeo Fukuda created the award in 1977. Japanese home run king Sadaharu Oh, the first recipient, took part in Sunday's ceremony.
Matsui played seven seasons for the Yankees, and was the MVP of the 2009 World Series, before finishing his career with a season each for the Los Angeles Angels, the Oakland Athletics and the Tampa Bay Rays.
Other recipients of the award include film director Akira Kurosawa and Japan's women's national soccer team that won the World Cup in 2011.