Hachiro described the area around the crippled Fukushima nuclear power plant a "shi no machi" or a "town of death".
But he denied media reports that after his visit to the nuclear plant, he pretended to rub his jacket against a journalist, while making a remark to the effect that "I will infect you with radiation".
The "town of death" comment was seen as particularly insensitive because the government cannot provide evacuated Fukushima residents with a firm timetable for their return, amid criticism over how it has handled the crisis.
Hachiro’s departure is an early blow for Prime Minister Yoshihiko Noda, Japan's sixth new prime minister in five years, who is
looking to restore momentum and morale following the resignation of the fiercely criticised Naoto Kan.
In a press conference on Saturday, Hachiro, 63, apologised repeatedly and said Noda had accepted his resignation, which came a day before Japan was to mark six months since the 11 March earthquake and tsunami, which left 20,000 dead or missing and sparked the nuclear crisis at Fukushima.
Noda had pledged his government would boost post-disaster recovery efforts but the early resignation of one of his cabinet ministers will do little to stem an erosion of faith in Japan's leaders following the March calamities.
Out of Noda's 17-member cabinet, 10 including Hachiro are newcomers to ministerial posts.