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The total cost from collapse or damage to houses, factories and infrastructure such as roads and bridges would be between 16 trillion yen and 25 trillion over the next three fiscal years, according to the Cabinet Office.
The damage could lower Japan's growth by 0.5 percent, it warned.
The figure compared with roughly 9.6 trillion yen damage from the Kobe quake in 1995.
The estimated figure covers seven prefectures of the hardest-hit areas of Iwate, Miyagi, and Fukushima, as well as Hokkaido, Aomori, Ibaraki, and Chiba.