All 17 beaches in the prefecture had been closed last summer amid concern over radioactive contamination following an earthquake and tsunami in March 2011, which wrecked Japan's Fukushima Daiichi nuclear plant and left almost 20,000 people dead.
Local authorities gave the all clear to Nakoso beach, 40 miles south of the nuclear power station, declaring the waters free of contamination. Officials said radiation detected in the water at the beach was negligible.
But on the same day as the beach was opened, tens of thousands of people rallied in Tokyo demanding that the government abandon nuclear power.
Crowds estimated at 200,000 gathered for a rally at Yoyogi Park in the capital.
Protesters expressed outrage over a report that blamed the Fukushima disaster on Japan's culture of "reflexive obedience" and held no individuals responsible.