When the governor of Miyagi, Yoshihiro Murai, arrived late, Matsumoto refused to shake his hand.
“You came in late. When a guest comes, you have to be here first before you call your guest into the room,” he told the governor.
Matsumoto then sought to bully journalists who had attended the event to keep the incident quiet.
But his comments were aired on TV, causing an outcry for his resignation. Miyagi, on the north-eastern coast of Japan, was devastated by the 11 March earthquake and tsunami.
The resignation is another blow for Japan’s Prime Minister Naoto Kan, who is also facing pressure to step down. He has promised to go soon, but only once several bills on disaster recovery and renewable energy have been passed.