Matsuoka had been sharply criticized for allegedly claiming false expenses. He was also accused of accepting donations from companies involved in a bid-rigging scandal. He denied doing anything wrong.
Opinion polls show the scandal may be one of the reasons for Prime Minister Shinzo Abe's plummeting popularity.
Japan's Kyodo news agency quotes Prime Minister Shinzo Abe saying Matsuoka was a competent minister of agriculture and the effects on the administration will be significant.
Local media report he left a note addressed to Prime Minister Shinzo Abe saying "I am sorry for causing this trouble." - VOA News