Toshikatsu Matsuoka, 62, was found in his apartment Monday unconscious and declared dead hours later. The death comes just ahead of upper house elections, and as support for Prime Minister Shinzo Abe's Cabinet is plunging.
An autopsy showed that Matsuoka died after hanging himself, according to a Tokyo Metropolitan Police official who spoke on customary condition of anonymity. The minister was found hanging from a door in his apartment earlier Monday, and he left a suicide note, according to local media reports.
Abe, looking shaken after visiting the hospital where Matsuoka died, said although the minister had been "under intense questioning" in parliament, he had continued to be a useful member of the Cabinet.
"I am very disappointed," he said. "When I saw his face, he seemed to be at peace."
Matsuoka, the first Cabinet minister to kill himself while in office since World War II, had faced criticism over a scandal involving suspicious bookkeeping practices and was scheduled to appear before a parliamentary committee Monday afternoon for further questioning.
He allegedly claimed more than 28 million yen ($236,600) in utility fees even though he rented a parliamentary office where utility costs are free. Matsuoka also faced separate scandals related to bid-rigging and political contributions.
Abe had defended Matsuoka, saying the agriculture minister reported to him all the alleged issues were properly handled and his dismissal was not needed. However, media reports said there were calls for his resignation within the ruling party.
"The minister has refused to provide a detailed explanation on the allegations, merely repeating that he is in line with the law," said an editorial in the Yomiuri newspaper published on Monday morning.
Matsuoka's death struck Abe's government ahead of elections for the upper house of parliament on July 22.
Abe's government was just hit by a fresh scandal last week over the missing pension payment records for more than 50 million people, who have been unable to get the money they are entitled to receive.
On Monday, support for the Cabinet hit its lowest level since he took office last year.
Approval of Abe's Cabinet fell to 32 percent, down 11 percentage points from a similar poll in April, according to a survey by the national newspaper Mainichi. A separate poll by the Nikkei business daily showed Abe's popularity falling to 41 percent, down 12 percentage points from the previous month.
Both cited dissatisfaction with the government's apparent loss of the pension payment records.
"This is a big blow for Abe's government," said political analyst Eiken Itagaki. "I believe Abe will struggle to maintain the slim majority the ruling coalition has in the upper house."
Matsuoka had been dogged by scandal.
He was forced to apologize just three days after taking office for not declaring 1 million yen ($8,500) in political donations from a scandal-linked group. He acknowledged the undeclared funds, which came as purchased tickets to a fundraising party, saying he was unaware that the contributions had not been reported.
The government announced that Environment Minister Masatoshi Wakabayashi would take the agriculture portfolio temporarily. The farm ministry commands a powerful position within the government and oversees some of the country's most controversial policies, including its scientific whaling program and strict restrictions on U.S. beef imports over mad cow fears.
Japan's suicide rate is among the highest in the industrialized world. More than 32,000 Japanese took their own lives in 2004, the bulk of them older Japanese suffering financial woes as the country struggled through a decade of economic stagnation.
By Mari Yamaguchi and Kozo Mizoguchi of The Associated Press.