Japanese leaders did not know the extent of the damage in the wake of the nuclear crisis after the massive quake and tsunami hit the Pacific nation even as they tried to play down the risk in public, an independent investigation is set to report.

Naoto Kan, the then-prime minister, and his staff began referring to a worst case scenario that could threaten Japan's existence as a nation around three days after the quake-triggered tsunami on March 11, and even secretly considered evacuating the capital, Tokyo, the report by the Rebuild Japan Initiative Foundation said on Tuesday.

The Japanese prime minister ordered workers to remain at the tsunami-crippled Fukushima nuclear plant as fears mounted of a "devil's chain reaction" that would force tens of millions of people to flee Tokyo, the report says.

That was when fears mounted that thousands of spent fuel rods stored at a damaged reactor would melt and spew radiation after a hydrogen explosion at an adjacent reactor building, according to the report.

In an interview with Reuters this month, the 65-year-old Kan said he was haunted by the spectre of a crisis spiralling out of control and forcing the evacuation of the Tokyo greater metropolitan area, 240km away and home to some 35 million people.