Agriculture Minister Toshikatsu Matsuoka, 62, committed suicide just hours before his scheduled interview with a parliamentary committee probing his role in a bid-rigging scandal.
He was found unconscious in his apartment shortly after noon Monday and immediately rushed to the hospital, but doctors at an intensive care unit failed to revive him.
The Police Agency did not disclose the text of Matsuoka's suicide notes, but said they contained apologies for his actions.
It was alleged that Matsuoka had accepted cash from companies in exchange for contracts with an environmental organization operating under his ministry.
Shortly after his appointment as agriculture minister in September 2006, he was also accused of failing to declare one million yen ($8,500) accepted as a political donation from a group suspected of illegal fundraising for investment projects.
Before taking up the ministerial post, he also faced accusations of claiming 142 million yen ($1.2 million) in back rent payments for an office he had been provided with for free as a member of parliament.
The prime minister tried to defend Matsuoka against calls for his dismissal, but his suicide is expected to further undermine support for Abe's Cabinet ahead of July 22 elections to parliament's upper house.
The incumbent government was dealt a serious blow in December when Administrative Reform Minister Genichiro Sata stepped down over alleged misuse of political funds.
