The tsunami alert, issued within minutes of last week’s earthquake, didn’t seem terribly ominous. But by the time it was lifted, fishing boats had been tossed ashore, coastal towns flooded.

Though Japan’s tsunami warning system is among the best in the world, even it came up woefully short in predicting what to expect from the magnitude 8.0 quake that rocked the northern island of Hokkaido on Sept. 26.

Measurements taken near Erimo, a town on Hokkaido’s southeastern tip, indicate that waves reached 4 meters high, said Fumihiko Imamura, a professor at Tohoku University’s Disaster Control Research Center.

That would make the tsunami twice as high as the government predicted.

“Erimo’s proximity to the quake’s epicenter, its exposure and the shape of the seabed off its coast contributed to the larger-than-expected waves,” he told a gathering of scientists Tuesday.

The findings underscore the difficulties of predicting tsunami.

“There are many false alarms and inaccurate predictions,” said Mikio Fujii, who sends out warnings from the Meteorological Agency. “Usually, we try to err on the side of caution.”

Located along the Pacific “Ring of Fire,” Japan is one of the world’s most earthquake-prone countries. Its precarious perch atop three tectonic plates — the chunks of land that collectively form the Earth’s crust — and its heavily populated coasts account for a long history of disasters caused by tsunami, which literally means “harbor waves.”

One of the earliest recorded tsunami was a wall of water that leveled the building around a giant statue of the Buddha in Kamakura, Kanagawa Prefecture, in 1498. Japan’s most devastating tsunami in recent history struck in 1896, killing more than 21,000 people.

The persistent threat of tsunami has led to a round-the-clock watch for the killer waves.

Japan has six regional tsunami information centers, which monitor offshore seismic activity. When a quake or undersea landslide occurs, a supercomputer program is used to make wave predictions based on epicenter and magnitude. Alerts can be issued within minutes.

Off-shore, fiber-optic pressure and tide sensors offer a second line of defense. Links with other country’s experts, such as the U.S. Pacific Tsunami Warning Center in Hawaii, provide another backup.

But scientists say predicting tsunami is all about refined guesswork.

It’s often impossible to know whether a tsunami will rise up and pound the shoreline or wash harmlessly onto the beach, because much depends on the topography of the seabed.

“You can’t predict a tsunami just by observing it,” said Yasuhiro Umeda, a seismologist at the Disaster Prevention Research Institute at Kyoto University. “Predictions are calculations that require data about the contours of the ocean floor. The more precise the data, the better the prediction.”

Unlike surface tides, tsunami can travel at great depths and at speeds of up to 800 kph. As the water becomes shallow, the waves, slowed by the upward slope, rise higher.

The limitation of prediction technology is that scientists don’t have precise ocean floor data, Umeda said.

Following last week’s magnitude-8 quake off Hokkaido, fishing boats littered a beach in Toyokoro. In nearby Tokachi, a trawler was lifted onto a pier, as wave after wave submerged the port town and wrecked nearby homes.

Two fisherman were missing in the aftermath, both believed to have been swept away by waves.

Most people who live along the coast are taught as youngsters to head for high ground after an earthquake strikes.

But last week, many who fled in cars got stuck in traffic jams. Others didn’t know in which direction to run, or weren’t aware of the location of evacuation centers, Imamura said. Some just stayed put.

The Meteorological Agency’s frequently overblown or incorrect warnings can give people a false sense of security.

“After warnings end up being false, people tend to lose faith in them,” Imamura said.

Sometimes, the warnings can’t come fast enough.

In 1993, residents on Okushiri Island, on the opposite side of Hokkaido from last week’s quake, had almost no time to react before a tsunami flattened their village. By the time tsunami alerts went out five minutes after the initial jolt, the waves had already crashed ashore.

More than 200 people died in the waves — the biggest measuring 30 meters tall — and fires triggered by the quake.

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