As the hours ticked by, bigger and bigger waves struck the Japanese coast.
Residents in the north island Hokkaido and the main island Honshu could do nothing more but wait for the danger to pass.
The massive magnitude-8.8 earthquake had already generated a powerful tsunami wave higher than 3 metres, battering Russia's remote Kamchatka Peninsula.
Buildings were damaged and a kindergarten collapsed. But there were no serious injuries.
In Japan, authorities braced for something similar.
The first wave was much smaller than predictions. Only 30 centimetres.
But Japan, well versed in the science of tsunamis, knew that was not the full picture.
An evacuation order covering some 2 million residents remained firm.
By lunchtime, the tsunami waves were well over a metre.
Fumihiko Imamura, a tsunami expert with the International Research Institute of Disaster Science, explained the first tsunami wave was often not the largest, making situations like that on Wednesday fluid and hard to predict.
"The first wave is followed by a second wave," he said.
"The later waves become bigger and stronger. There have been cases where the largest wave arrives half a day later."
Tsunami waves also do not behave like normal surf waves.
They swell with tremendous force and each cycle can last an hour.
'Evacuate now!'
The magnitude-8.8 earthquake erupted at a relatively shallow depth of under 20 kilometres.
The massive release of energy suddenly displaced water and generated a tsunami wave.
In Japan, the unmistakable sound of tsunami sirens gave residents the first warning of potential danger.
Towns and cities implemented their well-rehearsed tsunami measures with confidence.
Factories, airports, workplaces, and even the stricken Fukushima nuclear power plant shut down.
Residents used rooftops and hilltops as refuges as waters surged.
"Do not be glued to the screen," one reporter from the public broadcaster NHK ordered viewers.
"Evacuate now!"
Japan's Meteorological Agency warned tsunamis could continue to hit for a day or more.
The trouble is tsunami waves bounce of landmasses and collide with other tsunami waves.
The ocean churns and swells.
"The tsunami waves bouncing off various places all overlap," Professor Fumihiko explained.
"The later waves to grow stronger. Unfortunately, this is difficult to predict."
The Kamchatka Peninsular earthquake was the sixth-biggest on record.
In 1952, an even bigger earthquake struck the same region.
It took nine hours for the largest tsunami to reach Japan.
Japan better safe than sorry
Japan sits on top of four tectonic plates, making it one of the most seismically active countries.
It is well prepared.
Building standards are made to survive powerful quakes, while concrete fortifications along the coastline shield towns from tsunamis.
Residents in evacuation centres felt a sense of unease on Wednesday, but the situation remained relatively calm across the country.
"Disaster prevention education is being conducted in schools, and evacuation drills are held in communities," Professor Fumihiko said.
"This includes learning where to evacuate and how to cooperate with others."
Recovery work at the Fukushima Nuclear Power plant, devastated in the 2011 Tohoku earthquake and tsunami, was immediately put on hold.
The power plant's operators, TEPCO, soon confirmed there was no safety concern but it was taking precautionary measures.
In Japan, it is better to be safe than sorry.
By late evening, some parts of the island of Honshu had their tsunami warnings downgraded to advisories, while the warnings remained firm for other Pacific-facing territories.
The main injuries were not tsunami related — but rather due to people suffering from Japan's sweltering summer while complying with evacuation orders.
One woman died after she drove off a cliff while trying to reach an evacuation zone.
