Naoki Inose, who was elected head of one of the world's biggest cities a year ago, said he had handed his letter of resignation to the head of the assembly.
"I have decided to resign from the post of Tokyo governor," Inose told a hurriedly arranged press conference.
"I intended to fulfil my duty of explaining to the city assembly, people of Tokyo and people of the nation, but regrettably I could not clear doubts over me. It's solely because of my lack of virtue."