Wind-driven waves on Tuesday slammed into coastal barriers and storm surges flooded seaside towns. Japan's government sent 70 Self-Defence Force soldiers to fortify barriers, help evacuees and provide other help in storm-hit areas, said Chief Cabinet Secretary Hiroyuki Hosoda.
The typhoon grounded hundreds of flights, blocked train and ferry services and closed highways, stranding tens of thousands.
Nabi's winds were up to 126 km per hour as it made landfall and travelled up Japan's southernmost main island of Kyushu, the country's Meteorological Agency said. Heavy rain and wind pounded the neighbouring island of Shikoku.
"The wind and rain were so strong earlier this morning, I could hardly walk - I couldn't leave the building," said Mitoshi Shiroi from his flooded grocery store in Kyushu's Tarumizu town.
"The water just keeps on coming in from under the door," he said. Power outages hit more than 270,000 households in Kyushu, said Kyushu Electric Power Company spokesman Tetsuo Yano.
The typhoon forced Prime Minister Junichiro Koizumi to cut short a two-day campaign trip to western Japan ahead of 11 September national elections.
"The water just keeps on coming in from under the door"
He was set to return to Tokyo on Tuesday evening in an attempt to avoid the storm, a Liberal Democratic Party official said on condition of anonymity.
Three people were killed when landslides swept through their homes in Kagoshima, said prefectural (state) police official Hideaki Torigoe.
A landslide killed another man in neighboring Miyazaki prefecture, said local police official Takayoshi Tanaka.
Police in several Kyushu prefectures and on nearby Shikoku island said that 16 other people were missing and that more than 60,000 were ordered to evacuate their homes.
National broadcaster NHK reported that 51 people had been injured. Heavy weather was hindering efforts to rescue people trapped under landslides, officials said.
Ferry services were cancelled between South Korea and the Japanese city of Fukuoka, and between Kyushu and western Japan. Train services in southern Japan were also disrupted, with landslides burying some tracks, NHK reported.
Japan Airlines and its affiliates cancelled 307 flights on Tuesday - 10 on international routes - while All Nippon Airlines grounded 374 domestic flights.
Heavy rain expected
The cancellations affected more than 60,000 people, the two companies said.
Japan's Meteorological Agency said up to 50cm of rain was expected in Kyushu and Shikoku, as well as western Honshu island, by Wednesday.
Mitsubishi Heavy Industries Ltd. closed shipbuilding plants in Nagasaki, Yamaguchi and Hiroshima, affecting 11,800 employees, said company spokesman Takyoshi Furuya.
Mazda Motor Co. shut factories in Hiroshima and Yamaguchi, said company spokeswoman Mayumi Handa. She declined to say how many workers were affected.
Nabi, meaning butterfly in Korean, was expected to move northeast and become the first typhoon to hit South Korea this year. One or two typhoons usually affect the country annually.
Water has flooded the southern-
most Japanese island of Kyushi
In South Korea's southeastern port city of Pohang, the 5470-tonne Vietnamese cargo ship Long Xuyen ran aground after high waves swept it towards the beach, South Korea's Yonhap news agency said.
Its 22 crew members were safe, Yonhap said. An elderly South Korean is believed to have been swept away in a swollen river after falling from a bridge in the southern city of Ulsan, Yonhap said.
South Korean city
In South Korea's second-largest city, Busan, about 450km southeast of Seoul, winds downed dozens of signboards, uprooted trees and toppled a 10-metre-high advertising tower at an intersection, disrupting traffic, Yonhap said.
Busan had received up to 15mm of rain as of 2 pm on Tuesday. Last year, a record 10 typhoons and tropical storms struck Japan, leaving nearly 220 people dead or missing - the largest casualty toll since 1983.
Typhoon Tokage, which hit in October, was Japan's deadliest storm in more than a decade, killing 83 people. Scientists partially blamed last year's intense storm season on warmer-than-average ocean temperatures.