Shigenaga Tomioka, 56, set upon his older sister Nagako, chief priestess at Tomioka Hachimangu shrine, with a samurai sword late Thursday in a rare violent assault in the Japanese capital.
The 58-year-old Nagako was later pronounced dead with a "deep" stab wound to her chest along with a laceration to the back of her neck.
Shigenaga Tomioka had once served as a priest and the siblings had long quarrelled over shrine affairs, according to local media.
Police refrained from commenting on the motive but said it was not a random assault.
Nagako and Shigenaga are known to have fought over the succession rights at the shrine, local media said.
While Shigenaga was assaulting his sister, another woman -- reportedly the attacker's wife -- pursued Nagako's driver with a sword.
The driver escaped but suffered deep cuts to his shoulder, arm, and chest, police said.
After the attack, the pair then moved to an area near the residential compound on the shrine's leafy grounds.
"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.
The shrine dates back to 1627 and is best known for its summer water-splashing festival, seen as one of the top three festivals in Tokyo.
It has received Emperor Akihito and Empress Michiko in the past.
Sumo wrestlers also pay visits to the shrine, which had hosted tournaments in historic times.
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