In one of the most widely watched reforms to come out of the Fukushima accident, the government is moving to restore trust in regulatory oversight by separating Japan’s main nuclear regulatory agency from METI. In a bill now in Parliament, the government of Prime Minister Yoshihiko Noda wants to put the nuclear watchdog, the Nuclear and Industrial Safety Agency, known as NISA, into the more safety-minded Environmental Ministry as early as next month.

However, many here say targeting a single ministry does not go far enough in ending the murky links between government and industry. Critics like Mr. Koga, the former METI official, point to other, broader problems, such as the fact that Japan’s regulators are not nuclear specialists, but are reliant for expertise on the very companies they are charged with monitoring.

At the Japan Nuclear Energy Safety Organization, for example, a government agency that carries out safety inspections on behalf of NISA, most of the inspectors are former employees of the power companies and reactor manufacturers who often wink at safety lapses to protect their former employers, says Setsuo Fujiwara, a former inspector.

Mr. Fujiwara, who used to design reactors, said he clashed with supervisors over an audit he conducted in March 2009 at the Tomari nuclear plant on the northern island of Hokkaido. Mr. Fujiwara said he refused to approve a routine test by the plant’s operator, Hokkaido Electric Power, saying the test was flawed.

A week later, he said he was summoned by his boss, who ordered him to “correct” his written report to indicate that the test had been done properly. After Mr. Fujiwara refused, his employment contract was not renewed.

“They told me my job was just to approve reactors, not to raise doubts about them,” said Mr. Fujiwara, 62, who is now suing the safety organization to get rehired. In a written response to questions from The New York Times, the agency said it could not comment while the court case was under way.