Tokyo Metropolitan Police say the 59-year-old priest appears to have been ambushed by her younger brother and a female accomplice on Thursday night.
Police said that Nagako Tomioka, the 58-year-old head of Tomioka Hachimangu shrine, was attacked as she got out of her vehicle Thursday night.
Police have been searching for the attacker.
Her driver reportedly has also been wounded.
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 injuries to his shoulder and chest were not life-threatening. The brother then appears to have killed his accomplice before taking his own life.
After receiving emergency reports of a rampage with a blade, police rushed to the site and found four bleeding people near the shrine in the Tomioka district of Tokyo's Koto Ward.
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According to an acquaintance of a family member, Shigenaga was the chief priest of the shrine until he was dismissed about 10 years ago.
Shigenaga sent a threatening letter to his sister in 2006, saying he would "send her to hell", the Sankei newspaper said.
At the time, his sister had held a post known as negi, the second-highest rank at a Shinto shrine after the chief priest.
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.
Shigenaga is believed to have later stabbed the woman's chest and stomach before killing himself at the shrine, located about 400 meters east of Monzennakacho station on the Tozai subway line. The Tomioka Hachinangu shrine, established in 1927, has a close link with sumo and the emperor and empress visited in 2012.