Tokyo is all to set get its first woman governor in form of Yuriko Koike, exit polls projected today.
The former Japanese Defence Minister was forecasted as winner of the polls by the Japenese media.
One of the key challenges lying ahead of her will be curbing the financial problems plaguing Tokyo's preparations to host the 2020 Olympic Games.
Scandals linked to the Games forced the last two governors to resign.
"I will lead Tokyo politics in an unprecedented manner, a Tokyo you have never seen," Koike, 64, told her supporters.
In all, 21 contenders were vying to lead the sprawling capital and a number of other cities in the prefecture with Koike, politician Hiroya Masuda and journalist Shuntaro Torigoe being the the front-runners.
Today's election was called after previous governor Yoichi Masuzoe resigned last month following fierce criticism over allegations that he used official funds to pay for holidays, art and comic books for his children.
Masuzoe, who won election promising a scandal-free administration, denied breaking the law, but admitted to ethical lapses around his spending.
His predecessor, Naoki Inose also quit over a funding scandal in 2013, soon after Tokyo won the right to host the Olympics.
Since then Tokyo's preparations for the 2020 Summer Olympics have been hit by scandals, over-spending, administrative fumbles and construction delays.
One of the first duties of the new governor will be to travel to Rio at the end of the 2016 Olympics in August to accept the Olympic flag as the next host.
(With IANS inputs)