The first earthquake measuring 8.9 on the Richter Scale struck at 2.45 pm local time about 237 miles northeast of Tokyo at a depth of 15.2 miles, the US Geological Survey said, revising the magnitude from an earlier 7.9.
Ten nations are said to have issued tsunami-related alerts. Warnings have also been issued along the Pacific coast.
According to The Telegraph, among the countries that have issued a tsunami-related alert are Australia, Chile, Indonesia, Mexico, and the Mariana Islands, New Zealand, Peru, the Philippines, Russia and Taiwan. The Indian coastline has been declared safe as of now.
The Japanese Defence Ministry has sent up ten aircraft to obtain an aerial survey of the damage caused by the wave, which early warnings said could be up to 10 meters high.
Along Japan's coast, television footage showed massive damage from the tsunami, with dozens of cars, boats and even buildings being carried along by waters.
In Tokyo the car park of Disneyland was reported flooded.
A large ship was swept away by the tsunami and rammed directly into a breakwater in Kesennuma city in Miyagi prefecture, according to footage on public broadcaster NHK.
In Tokyo several fires were reported and the underground railway was evacuated. More than four million buildings reported a loss of electricity in the wake of the calamity.
In downtown Tokyo, large buildings shook violently and workers poured into the street for safety. TV footage showed a large building on fire and bellowing smoke in the Odaiba district of Tokyo.
In central Tokyo, trains were stopped and passengers walked along the tracks to platforms.
Footage on NHK from their Sendai office showed employees stumbling around and books and papers crashing from desks.
Thirty minutes after the quake, tall buildings were still swaying in Tokyo and mobile phone networks were not working. Japan's Coast Guard has set up task force and officials are standing by for emergency contingencies.
Several quakes had hit the same region in recent days, including a 7.3 magnitude one on Wednesday.
Japan's Earthquake Research Committee has warned of a 70 per cent chance that a great, magnitude-eight quake would strike Tokyo within the next 30 years.
The last major quake to hit Tokyo was in 1923, when the Great Kanto Earthquake claimed more than 140,000 lives, many of them in fires.
In 1855, the Ansei Edo quake also devastated the city. More recently, the 1995 Kobe earthquake killed more then 6,400 people.