The priestess, named in Japanese media as 58-year-old Nagako Tomioka was on the way to the shrine and was attacked when stepping out of her auto.
A violent attack with Japanese swords and survival knives at Tokyo's famed Tomioka Hachimangu shrine has left three dead - including the chief priestess and her brother - in an apparent family feud that turned deadly.
Her driver reportedly has also been wounded.
"We believe the male suspect (Shigenaga) stabbed the woman before stabbing himself", the spokesman said, adding that they both died, bringing the total fatalities to three.
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Shigenaga's partner, meanwhile, chased down his sister's driver, who had tried to escape on foot, and attacked him about 100 meters away. The driver's injuries were not life-threatening. The brother then appears to have killed his accomplice before taking his own life.
The assailant, identified as 56-year-old Shigenaga Tomioka, attacked his 58-year-old sister sister Nagako Tomioka, the shrine's chief priestess, with a Samurai sword and killed her after she got off from a chauffeur-driven vehicle.
Founded in 1627, Tomioka Hachimangu Shrine is located about 300 meters from Tokyo Metro's Monzen-Nakacho Station.
Shigenaga sent a threatening letter to his sister in 2006, saying he would "send her to hell", the Sankei newspaper said. The almost 400-year-old shrine is known for its close ties to sumo and holding one of Tokyo's three big Shinto festivals. The shrine left the association on September 28 this year.
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