The motive was unclear, though Japanese media reported there may have been a feud between the priest and her brother.
One man and one woman were killed and two others injured on Thursday night in a knife attack in Tokyo, local police said.
The attack began around 8:25 p.m., when Shigenaga Tomioka attacked his sister with a Japanese sword as she exited her vehicle on the shrine grounds.
The suspect is thought to have first killed his sister, the chief priestess at the shrine, said Kyodo news agency citing police.
The accomplice attacked the driver with a samurai sword and pursued him as he ran out of the temple grounds and about 300 feet down a road, police said.
The driver escaped but suffered deep cuts to his shoulder, arm, and chest, police said.
The incident occurred around 8:30 p.m. local time at the Tomioka Hachimangu Shinto shrine in Koto Ward, Tokyo.
Also, a woman aged in her 30s who was with Shigenaga Tomoika attacked and stabbed the driver of the vehicle with a Japanese sword, police said.
According to an acquaintance of a family member, Shigenaga was the chief priest of the shrine until he was dismissed about 10 years ago.
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. The shrine, located roughly 100 meters east of Monzen-Nakacho Station, is also the birthplace of the Edo-period fundraising sumo.