Voters in the Japanese capital elected their first woman governor on Sunday, after two predecessors stepped down over scandals that clouded the city's preparations to host the 2020 summer Olympic Games.

Yuriko Koike, Japan's first female defence minister, beat former bureaucrat and fellow member of Prime Minister Shinzo Abe's party Hiroya Masuda, as well as liberal journalist Shuntaro Torigoe, according to an exit poll by public broadcaster NHK.

Koike, 64, angered the Tokyo branch of Abe's Liberal Democratic Party by not getting its approval before announcing her candidacy for city governor. The LDP instead drafted Masuda, 64, who once served as governor of a rural prefecture.

"Taking this result very heavily, as the new governor I would like move forward firmly with the administration of the metropolis," Koike, an experienced politician fluent in English and Arabic, told supporters.

"I would like to move forward with a metropolitan administration such as has never happened, never been seen, together with all of you."

The NHK exit poll showed Masuda was in second place, with Torigoe, a 76-year-old cancer survivor who was backed by several opposition parties, trailed both.

The sprawling city of some 13.5 million people faces a plethora of problems such as an aging population, daycare shortage, and the ever-present possibility of a big earthquake.

But a big issue in the campaign was the 2020 Olympics, which Japan hopes will spur its economy, struggling to escape decades of deflation.

Construction of the main stadium has been delayed and the original logo for the games had to be scrapped after plagiarism accusations.

After the resignations of the city's two previous governors, Koike will be responsible for saving Tokyo's reputation as host for the games.

One of her first duties will be to travel to Rio de Janeiro when the curtain comes down on next month's games there to accept the Olympic flag as the next host.

"The Olympics are right in front of us. I want to use them as a chance to build a new Tokyo for beyond 2020," Koike said when the campaign began.

Though the LDP and its coalition partner backed Masuda, fallout for Abe will likely be minimal despite Masuda's loss.

"This is basically a Tokyo issue," said Kenji Yumoto, vice chairman of the Japan Research Institute think-tank. "Abe's prestige probably won't be damaged and support for the LDP won't fall."