The Kashiwazaki-Kariwa plant in Niigata prefecture, some 250 kilometres (155 miles) northwest of Tokyo, leaked a small amount of radioactive water after a 6.8 Richter-scale earthquake on July 16.
The plant's operator said the amount of radiation from the nuclear plant, which is the largest in the world, was far too little to cause health concerns. But it came under criticism for initially under reporting the level.
Kenzo Miya, an engineering professor at Tokyo's Hosei University and since 2003 the head of a prefectural commission on the plant's safety, inspected the site and found no risk.
He said Thursday at a press conference that the earthquake was an "irreplaceable, invaluable experiment."
"Mr. Miya has resigned citing unspecified personal reasons," a prefectural official, Shinichi Fujita, told AFP.
Asked if his resignation was due to the faux pas, Fujita said: "You may imagine many things about the matter, but we cannot say."
The earthquake destroyed hundreds of homes and killed 11 people.
In a bid to assuage concern about the radiation, Japan has invited a team from the UN International Atomic Energy Agency to inspect the plant next week.
Miya's was the latest gaffe to make headlines in Japan.
Earlier this year, the defence minister resigned after saying that the nuclear attacks on Hiroshima and Nagasaki hastened the end of World War II.