In June 2003, Matsui was selected the Japan national team for 2003 Confederations Cup. At this tournament, he debuted against Colombia on June 22. He was also selected Japan U-23 national team for 2004 Summer Olympics. From 2008, he played many matches under manager Takeshi Okada. In 2010, he was selected Japan for 2010 World Cup. He played all 4 matches and Japan qualified to the knockout stage. He also played at 2011 Asian Cup and Japan won the champions. This Asian Cup was his last game for Japan. He played 31 games and scored 1 goal for Japan until 2011.
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