Japan plans to spend 1 trillion yen on nationwide disaster prevention, including strengthening levies, in the fiscal year that started on April 1, according to the transport ministry.

Should the Arakawa break its banks, about 2,000 people in Tokyo may lose their lives and 860,000 will be stranded, according to the government. Water would flood subway and regular train lines, crippling 97 stations.

One of Tokyo's largest wards, Edogawa City, which is sandwiched between the Arakawa and Edogawa rivers, predicted it would cost 1.7 trillion yen to strengthen and rebuild the banks to prevent breaching during a flood, said Naomasa Tachihara, director of Edogawa's department of public works planning.

In Tokyo in 1947, about 1,100 people died and 31,000 houses were destroyed when Typhoon Kathleen hit and caused the Tonegawa River north of the city to break its banks, according to the Cabinet Office. A repeat of that flood today with a larger concentration of people and property in the capital would cause catastrophic damage.

A tidal storm surge in Tokyo Bay may be the most devastating for the capital, leading to about 7,600 deaths and the flooding of an area housing 1.4 million people, according to government estimates.

Metropolitan Tokyo, which spreads out around a bay and covers an area of 1,782 square kilometres, eclipsed New York- Newark as the world's most highly populated area in 1975. Now it has 35 million people.

Edogawa, the fifth-most populated of Tokyo's 23 districts or wards, was most at risk because it was penned in by the Arakawa on one side, the Edogawa on the other and faced Tokyo Bay, said Tachihara from the public works planning department.

"Edogawa is shaped like a basin, with the levees being the edges," he said. "Without levees 70 per cent of Edogawa would be under water in a storm."

Tokyo has spent centuries changing the course of rivers and building levee banks to reduce flooding.

Shogun Ieyasu Tokugawa, the first samurai to unite Japan in 1600 and who became shogun three years later, ordered river diversions 400 years ago. He decided to change the course of the Tonegawa, Japan's second-longest river, so it flowed into the Pacific Ocean rather than through Tokyo, then known as Edo.

The task took three generations to complete, with Ieyasu's grandson Tokugawa Iemitsu finishing the job, according to the Geotechnical Society's Sueoka.

"Tokyo has been building defences against floods since the Edo government," said Tachihara. "What we're doing now is for the future. We're preparing for a once-in-200-years event."

About 40 kilometres north of Tokyo is another flood protection project, the Metropolitan Area Outer Underground Discharge Channel. A shaft tall enough to house the Statue of Liberty has been built to feed water from five rivers into a reservoir carved underground. The space, big enough to hold four Parthenons, is supported by 59 columns each weighing 500 tonnes.

A 6.3-kilometre underground tunnel draws floodwaters to the reservoir, which has four of the engines used on Boeing 737 passenger jets to pump away up to 200 cubic metres of water a second.

"The amount of flooding in the area has dropped significantly since we started operations," said Takashi Komiyama, who manages the facilities, which took 13 years and 230 billion yen to build.

"We used to be prepared for about 50 millimetres of rain an hour, but now we need to be ready for 100 millimetres or 120 millimetres," said the geotechnical society's Sueoka. "It's difficult to think in terms of 100 or 200 years to secure the nation's safety, but that's what it takes."