Governor Yoichi Masuzoe accused of using public money for family trips, expensive hotels and artwork.
The governor of Tokyo has submitted his resignation after weeks of pressure on him to step down over allegations of misusing public funds.
Yoichi Masuzoe, who announced his decision to quit on Wednesday, was facing a no-confidence motion that was set to be introduced later the same day.
The governor had come under intense questioning in the Tokyo Metropolitan Assembly for allegedly using the money for family trips, artwork and other expenses.
The resignation will take effect on June 21.
His troubles began earlier this year with revelations that he had stayed in expensive hotel suites at the taxpayers' expense on working trips to Europe and the United States.
Investigators looking into allegations of misuse of funds found that his use of the money was inappropriate but not illegal.
Masuzoe, who faced repeated grilling by the legislature and in the media, had admitted to ethical lapses but denied breaking any laws.
In a short speech before the Tokyo legislature, a chastened Masuzoe said he had worked hard for the 2020 Olympics and was filled with regret.
"But I am responsible for all of this," he said.
Lawmakers approved his resignation, shortly before he spoke.
"The ruling Liberal Democratic Party of Japan (LDP) is embarked on a damage control exercise," said McBride, "They had supported the governor for the election".
"There are all important upper house elections coming up next month, and LDP general Secretary today have been apologising to the citizens of Tokyo."
Masuzoe, a former health minister backed by Japan's ruling party, easily won an election in February 2014 and promised a successful 2020 Olympics.
He balked at the high cost of the Games, and successfully lobbied to have some events moved to existing facilities in farther-out areas, instead of building new ones in Tokyo.
The governor had asked for a suspension of the investigation until after this year's Games in Rio de Janeiro.
Masuzoe's predecessor, Naoki Inose, also resigned due to a money-related scandal in December 2013 after revelations that he had received $480,200 from a hospital company.
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