Tomakomai Mayor Tadashi Sakurai submitted a letter of resignation Monday to the municipal assembly following allegations he groped the owner of a local restaurant, city officials said.
The resignation will take effect May 31.
An election to select his successor has to take place by early July in line with the Public Offices Election Law.
Sakurai, 52, admitted last week he groped the woman while he was drunk earlier this month.
The woman has filed a criminal complaint with police.