Land deemed free of harmful radioactivity and safe for the city to occupy has now come under question as the scandal over the purported cleanup of San Francisco’s biggest redevelopment site continues to grow.

On four portions of the former Hunters Point Naval Shipyard — an EPA Superfund waste site — almost all of the radioactivity measurements that were used to confirm the soil’s safety are “suspect,” according to a newly released analysis by the U.S. Environmental Protection Agency and two state agencies.

The measurements were collected by the Navy contractor Tetra Tech. The EPA discovered “a widespread pattern of practices that appear to show deliberate falsification.” The Navy earlier flagged signs of fraud in the same data.

Over the past year, the Navy and EPA have found similar problems with soil data in other parcels at the shipyard. But those parcels haven’t been handed off to the city for development to begin. This is the first time that regulators have discovered evidence of probable fraud in shipyard land that was already turned over to the city.

Although the four parcels in question are relatively small, they sit next to a 75-acre tract known as Parcel A, where a developer already has built about 300 homes and where people live and work. Because by federal law no land at the site can be transferred to the city without extensive checks for pollution, the transfer of these parcels points to broader dysfunction in the vetting process for all land at the former shipyard.

The EPA documented its findings in a March report that was sent to several public agencies, including the San Francisco Department of Public Health, which is responsible for monitoring the cleanup. However, the report was not released by the EPA or the city. Instead it was obtained through a Freedom of Information Act request by Public Employees for Environmental Responsibility, an environmental watchdog in Washington, D.C.

“This is a situation that is sort of spiraling down,” said Jeff Ruch, executive director of the environmental group.

The report contradicts the city’s recent assurances that the shipyard is safe. During a tour of Parcel A on Wednesday, Amy Brownell, an environmental engineer with the city’s health department, told The Chronicle that “the contamination has been cleaned up” across the shipyard. “We can say definitively there are no public safety concerns or health concerns out here,” she added.

Brownell, who has worked on the shipyard cleanup for 25 years, was copied on the EPA report that found fresh signs of fraud and raised new questions.

“Your city public health officials would be the last people you’d want in denial,” Ruch said. “You shouldn’t have responsible city officials dissembling and suggesting that there aren’t problems here when they’re being told, quite explicitly, these are problems.”

In an email, health department spokeswoman Rachael Kagan pointed to EPA statements “verifying the health and safety of the Shipyard” and said her department supports “a reevaluation of the Parcel A site” by the state. “The DPH is 100% committed to protecting and promoting the health of everyone in San Francisco,” she wrote. Brownell did not return emails and a phone call.

The environmental group’s release of the report follows weeks of calls by alarmed residents to retest Parcel A. It also comes on the heels of criminal charges against cleanup managers on the shipyard project. In 2017, two former supervisors for Tetra Tech, the Navy’s main cleanup contractor, pleaded guilty to swapping contaminated dirt with clean soil to make it appear that tainted areas were free of harmful radiation. They were both sentenced to eight months in prison.

The shipyard’s history with radioactivity began decades ago when ships that had been used in the Pacific during nuclear bomb tests were brought to San Francisco to be cleaned with sandblast grit. From 1946 to 1969, the shipyard also housed the Naval Radiological Defense Laboratory, which used radioactive materials on rats, dogs and other animals to determine the effects of radiation on living organisms. The experiments produced barrels of radioactive waste and leached radioactivity into the buildings, pipes and soil.

Most shipyard operations ceased in 1974, and it was shut down as part of the U.S. Base Realignment and Closure process in 1991.

Since then, the Navy and San Francisco have been trying to orchestrate a federal cleanup and transfer of the shipyard, where a developer hopes to build more than 10,500 housing units, a hotel, schools and retail space on about 500 acres.

But questions over the accuracy of Tetra Tech’s soil tests emerged in 2012 when the Navy flagged anomalies in the soil data gathered on one piece of the site.

Despite that discovery — and a chorus of whistle-blowers who repeatedly told regulators and media outlets that Tetra Tech was lying — the $1 billion cleanup sped forward. The Navy allowed Tetra Tech to investigate and essentially exonerate itself, and the Navy and regulators continued to let Tetra Tech vouch for the safety of other pieces of the site, including the parcels now in question.

One of the parcels, known as D-2, bulges up to Parcel A along its southern edge. The other three are “utility corridors” that touch Parcel A, thin strips of land called UC-1, UC-2 and UC-3. While UC-3 is still owned by the Navy, the other three parcels were transferred in 2015 to the city’s Office of Community Investment and Infrastructure.

Tetra Tech was heavily involved. Not only did the company collect the radiation data on those parcels, Tetra Tech entities also wrote the official documents that declared the parcels suitable for transfer to the city. And regulators signed off.

“The safety of anyone who lives there or intends to live or work there is dependent on accurate measurements and thorough regulatory oversight,” said Daniel Hirsch, retired director of the environmental and nuclear policy program at UC Santa Cruz. “And all of that broke down here. The land transferred when the measurements were almost entirely fraudulent. And every aspect of the review failed to catch it.”

The four questionable parcels next to Parcel A are separated from inhabited areas by fences. Lennar Corp., the master developer of the site, is not currently doing construction there, according to Nadia Sesay, executive director of the city’s investment and infrastructure agency.

In an interview Saturday, Sesay said she is troubled by the findings in the EPA report, “and we will hold the Navy and the regulatory agencies accountable.”

“We want them, at the minimum, to clean the sites,” she said. “We just want them clean.”

Jason Fagone and Cynthia Dizikes are San Francisco Chronicle staff writers. Email: jason.fagone@sfchronicle.com, cdizikes@sfchronicle.com Twitter: @jfagone, @cdizikes