Tomioka then fatally stabbed his girlfriend and committed suicide with the weapon used in the attack, according to the police, who reached the scene of the crime after receiving calls from residents.
Police said that Nagako Tomioka, the 58-year-old head of Tomioka Hachimangu shrine, was attacked as she got out of her auto Thursday night.
After slashing the priestess, Shigenaga Tomioka then stabbed the younger woman to death with a sword, before killing himself, police said.
An apparent murder-suicide involving a samurai sword at a Tokyo religious shrine has left the head priestess dead, along with her assailant brother and his girlfriend.
Kyodo news agency reported there was some kind of confrontation between the priestess and her brother, named as Shigenaga Tomioka. The injuries to his shoulder and chest were not life-threatening.
A blood-stained samurai sword and survival knife were retrieved from the scene.
Founded in 1627, Tomioka Hachimangu Shrine is located about 300 meters from Tokyo Metro's Monzen-Nakacho Station.
The Tomioka Hachimangu shrine, established in 1927, has a close link with sumo and the emperor and empress visited in 2012.
Tomioka was chief priest of Tomioka Hachiman shrine.
Shigenaga Tomioka was arrested some 10 years ago for blackmailing his sister.
Shigenaga sent a threatening letter to his sister in 2006, saying he would "send her to hell", the Sankei newspaper said. It is known as the birthplace of sumo.
The Times says authorities suspect a dispute between the brother and sister over the Shinto shrine's chief priest position. The shrine left the association on September 28 this year.
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