The findings, announced Friday, led to an infuriated Tokyo Gov. Yuriko Koike proposing protections for whistleblowers to prevent such cover-ups.

She said the probe failed in its principal aim: to determine why a thick layer of clean soil was never laid at the site. Instead, empty basements are now subject to water welling up and bringing with it toxins such as arsenic, cyanide and benzene.

“Officials and staffers responsible for the project continuously misinformed Tokyo Metropolitan Assembly members, Tokyo residents and market staffers,” she told reporters. “I have to say, they failed to fulfill their responsibilities.”

The site was selected in 2007 to replace the aging Tsukiji fish market, with toxins detected there the following year. Construction of new market buildings was supposed to include remediation work to reduce the risk of contamination.

The governor said the investigation was such a whitewash that it cannot form the basis for reforms of the metropolitan administration and prevent similar scandals in the future.

Instead, she said Tokyo needs whistleblowers and urged them to come forward. She said she would introduce a system that protects such activity in future.

She said the case is not done yet, as she plans to cross-question previous governors and other officials who handled the Toyosu project.

The new market building was supposed to stand on a 4.5-meter-thick layer of clean soil. This plan was later modified five times, Koike said, leading to the current situation where facilities earmarked for seafood and fruit and vegetable dealers have nothing beneath them but an empty basement with a thin concrete floor covered with water containing traces of benzene and arsenic.

Measurements at the greengrocer section released Thursday showed the toxin levels slightly exceed safety limits: benzene and arsenic were 0.014 milligrams and 0.011 milligrams per liter at two locations, exceeding the safe standard of 0.01 milligram.

Similar surveys had been carried out seven times since November 2014, but this is the first time toxic substances have been found to exceed safe levels.

Koike said a decision on whether the site is safe to house merchants from Tsukiji will be made after tests are carried out in November. Those results will be released in January at the earliest. “The market cannot function if safety is not ensured,” she said.

But he never doubted the importance of such fundamental scientific studies, a belief that eventually achieved great progress in the life sciences that helped unlock key mysteries of autophagy, the process of removing unwanted proteins within a cell.

“I want to emphasize one thing here. When I started this study, I wasn’t convinced that this would lead to (answers for) any questions such as those concerning cancer and human longevity,” Ohsumi, an honorary professor at the Tokyo Institute of Technology, said during a news conference at the university Monday evening.

“I really hope people will understand that studies in fundamental sciences can achieve progress like this,” Ohsumi said.

His achievements in autophagy came through his work in yeast.

When yeast is starved for nutrition, it starts degrading its own proteins — a phenomenon Ohsumi observed with his own eyes through an optical microscope.

This process of autophagy can be widely seen in various creatures, including humans, plants and even microorganisms.

During the news conference, Ohsumi pointed out a human produces far more proteins every day inside the body than the amount that can be made from amino acids obtained from proteins he or she eats.

This shows the degradation and recycling of its own protein is a fundamental body function that supports our own life, he said.

“Thanks to Ohsumi and others following in his footsteps, we now know that autophagy controls important physiological functions where cellular components need to be degraded and recycled,” the Nobel committee said in a press release.

“Autophagy can rapidly provide fuel for energy and building blocks for renewal of cellular components, and is therefore essential for the cellular response to starvation and other types of stress,” it said.

During the news conference, Ohsumi lamented that in Japan today, scientists often face pressure to achieve quick results “that are useful for something,” such as those that can be used for practical medical treatments within mere years.

However, some achievements in fundamental scientific studies may not prove “useful” to other researchers for another 10 or 100 years, Ohsumi said.

He said he hopes science will be regarded as important in its own right, “not something that is developed for practical purpose only.”