On 31 March 1999, Morioka debuted for Japan national team against Brazil. After the debut, he became a regular player and played all matches including 1999 Copa America in 1999. He mainly played as central defender in three back as Masami Ihara successor. He also served as captain in many matches. In September 2000, he was elected Japan U-23 national team as over age for 2000 Summer Olympics. He played 3 games as captain. In October, he played at 2000 Asian Cup. He played full-time in all 6 matches and Japan won the champions. He also played at 2001 Confederations Cup and Japan won the 2nd place. In 2002, he could not play for injury. He was elected Japan for 2002 World Cup. He played as captain in first match against Belgium, but he was injured and replaced. After 2002 World Cup, in March 2003, he was elected Japan again by new manager Zico. On 8 June 2003, the match against Argentina is his last game for Japan. Although he was a member of Japan for 2003 Confederations Cup in June, he did not play in the match. He played 38 games for Japan until 2003.