The Port and Airport Research Institute recorded the massive tsunami in Ofunato, Iwate prefecture that swept away an entire town.
Japan's biggest-ever tsunami was recorded at 38.2-metres high in a massive 1896 earthquake.
An official with the institute said that without the coastal levee that did not exist in 1896, the latest tsunami was likely to be the biggest ever to hit Japan.
The study was conducted Friday using global positioning system GPS and measuring instruments.
The Geospatial Information Authority of Japan said that at least some 400 square kilometers of land were flooded in the March 11 tsunami.
The figure may be revised upward as the survey using aerial photos has yet to analyse 20 percent of the affected area.
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