A 91-year-old woman was found dead after being buried by a rain-triggered mudslide in Hanamaki, Iwate prefecture, according to Japan's national broadcaster NHK and Jiji Press.
Meanwhile, a 62-year-old man died after he was swept away by a swollen river in Nichiwaga, in the same prefecture, Kyodo news agency said.
News reports also said five residents remained unaccounted for while three others were injured in the neighbouring Akita Prefecture after their houses were swept away by massive floods.
The meteorological agency issued evacuation warnings for residents in the region, calling on them to take "immediate action" to protect their lives.
The Iwate local government has asked Japanese troops to assist in emergency related operations, Kyodo News reported.