Matsunaga was capped 40 times for Japan national team between 1988 and 1995. He was the first-choice GK when Japan won the 1992 Asian Cup. However, he was sent off for retaliation in the semi-final against China and Kazuya Maekawa filled in for him for the rest of the competition. He was also tending the goal when Japan's hope to play in the 1994 World Cup finals was dashed by a late Iraqi equaliser in the 1994 World Cup qualification final qualifier, the match that the Japanese fans now refer to as the "Agony of Doha" ().