The suspect is thought to have first killed his sister, the chief priestess at the shrine, said Kyodo news agency citing police.
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.
Also, a woman aged in her 30s who was with Shigenaga Tomioka attacked and stabbed the driver of the vehicle with another katana, police said.
Japanese media reports said he was her younger brother and that the attack was part of a family feud.
Nagako Tomioka, 58, chief priestess of Tomioka Hachimangū in Tokyo, was attacked by Shigenaga Tomioka, 56, as she got out of a auto on Thursday evening.
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Her driver reportedly has also been wounded.
Authorities suspect a row between the brother and sister over the shine's chief priest position had prompted the apparent murder-suicide.
Shigenaga and the other woman, who was his girlfriend and believed to be in her 30s, apparently ambushed Nagako after she got out of a vehicle on the grounds of the shrine in Tokyo's eastern ward of Koto.
According to police, Shigenaga Tomioka, 56, who was accompanied by his girlfriend, aged in her 30s, used a Japanese sword to fatally slash the head and chest of Nagako Tomioka, 58, who is his sister and the chief priest of the shrine, after she exited a vehicle.
Founded in 1627, Tomioka Hachimangu Shrine is located about 300 meters from Tokyo Metro's Monzen-Nakacho Station. His injuries were nonetheless non-life threatening, the 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.