More than 360mm of rain fell in the 24 hours to Friday in parts of Chiba prefecture, which adjoins the capital Tokyo, inundating roads and railways and knocking out power to nearly 25,000 households during one of Japan's busiest holiday weeks.
Authorities said four deaths have been confirmed, including at least one person trapped in a submerged vehicle.
Soldiers have been dispatched to the area to help with relief efforts.
"This case was an extremely unusual situation, even by Japan's historical weather standards," Chiba Governor Toshihito Kumagai told reporters on Friday.
"I have responded to many disasters in the past, but I have never experienced a case like this."
The transport disruption left around 7000 people stranded at Narita, an airport spokesperson said, adding that all flights are scheduled to operate normally on Friday. Japan Airlines said some flights may experience delays but no cancellations are currently expected.
Major highways in Chiba, including routes linking Narita airport, one of Japan's main international transport hubs, with central Tokyo, remained closed, forcing drivers onto alternative routes and causing heavy traffic, according to highway operator NEXCO East.
Several rail services remained suspended on Friday morning, though some trains connecting Narita to Tokyo had resumed operations.
