TOKYO — Seismologists said Wednesday that a nuclear reactor in Tsuruga, in western Japan, stands above an active seismic fault, a finding that could lead to the first permanent shutdown of a reactor since the Fukushima crisis two years ago.

Japan’s newly installed Nuclear Regulation Authority also said Wednesday that it would issue an order that would effectively keep a separate unit, the Monju experimental fast-breeder reactor, closed until its operator overhauled safety measures at the site.

Any move to decommission the Tsuruga commercial reactor would deal a blow to Prime Minister Shinzo Abe’s efforts to get the country’s nuclear program back online. So would yet another delay in restarting the troubled Monju experimental reactor, which is a major part of Japan’s longstanding goal of creating a system to recycle nuclear fuel.

But those steps would show that the country’s new nuclear regulator, put in place to bolster oversight of the nuclear industry after the 2011 disaster, has teeth. Its predecessor was criticized for its close industry ties and a lax approach to safety.

“It is really just a matter of luck that there hasn’t been an accident” at Tsuruga, said Kunihiko Shimazaki, the head of a panel of seismologists assessing the fault that runs beneath it, according to Reuters.

Still, both the Tsuruga and Monju plants in Fukui Prefecture, even if off-line, could continue to face risks from a possible earthquake along the active fault.

Almost 3,000 spent uranium fuel rods are stored at the Tsuruga plant, while the Monju site stores plutonium fuel. Some experts suspect that Monju also sits atop an active fault.

All of Japan’s 50 commercial reactors were closed for inspections after the multiple meltdowns at the Fukushima Daiichi station, which forced the evacuation of more than 100,000 people. Since then, only two have been restarted.

The fate of the country’s reactors depends on safety assessments being carried out by the new regulatory agency, which has been studying the safety risks faced by those reactors.

The agency faces considerable pressure from Japan’s power industry, businesses and pro-nuclear politicians in Abe’s governing party to allow more reactors to restart.

Keeping the reactors closed has led to significant financial losses for power companies, which have been forced to make up for the power shortfall with expensive fossil fuel imports. The blow of a permanent closing could make some power companies insolvent.

Several power companies have said that they intend to restart their nuclear reactors this year, providing that they pass safety checks.

The Japan Atomic Power Co., which operates the two-reactor Tsuruga station, has contended that the fault is not active. The company could not immediately be reached for comment.

Dozens of governing party lawmakers formed a group Tuesday to push for the resumption of Japan’s idled nuclear reactors, saying that Japan’s economic recovery depended on a stable power supply.

Large manufacturers in Japan have warned that rising energy costs will hurt business.

In Wednesday’s announcement, seismologists directed by the regulatory authority to study a known fault that runs under the Tsuruga No. 2 reactor said that the fault showed signs of being geologically active, suggesting a high earthquake risk.

The authority’s chairman, Shunichi Tanaka, said last year that he would not allow the reactor to go back online if the faults were found to be active. But the authority does not have legal power to order a permanent shutdown, a situation that could leave the reactor in limbo.

It was not clear how the other reactor at the Tsuruga site, and two more under construction, would be affected by the authority’s decision on the No. 2 reactor.

The authority is also assessing faults under five other reactors across earthquake-prone Japan, and the results are expected in coming weeks.

In a separate report released Wednesday, the Nuclear Regulation Authority said it was barring the operator of the Monju experimental reactor from beginning work to restart the unit until it overhauled its approach to safety. The authority said it believed that Monju’s operator, the government-backed Japan Atomic Energy Agency, “could not sufficiently secure the safety of Monju,” and added that it saw “a deterioration in its safety culture.”

The Kyodo News agency quoted an unnamed official at the agency as saying that additional inspections at the plant would take at least until January next year.

Monju’s operator revealed last year that it had not properly inspected more than 10,000 devices at the experimental reactor, including those deemed important to safety.

The Monju reactor forms the cornerstone of a national project by Japan to reuse and eventually produce nuclear fuel. But the plant, a $12 billion project, has a history of safety lapses. It was closed for 14 years after a devastating fire in 1995, one of Japan’s most serious nuclear accidents before the Fukushima crisis.

Monju was reopened in May 2010, but just three months later, a 3.3-ton fuel relay device fell into the reactor’s pressure vessel, forcing it to close again. In the two decades since the reactor started tests in 1991, the atomic energy agency has managed to generate electricity at the reactor for only one full hour.