When the Navy began cleaning up its toxic shipyard in San Francisco in the 1990s, officials made a promise: The site would be scrubbed to the highest standards, essentially returned to its state before Cold War nuclear waste and industrial shops tainted the land.

But more recently, the Navy has ditched that plan for a cheaper approach that would leave much more contamination in the ground, according to a report released Tuesday by the Committee to Bridge the Gap, a nonprofit watchdog group on nuclear issues that often criticizes government and industry for their handling of hazardous waste.

The Navy lowered the standards even though city voters and elected officials demanded in 2000 and 2001 that the site be fully cleaned, the report points out. At the time, supervisors argued that looser rules could expose people to cancer-causing substances once the former Hunters Point Naval Shipyard was turned into a massive housing development.

Since then, in areas of the shipyard slated to become homes, businesses and parks, the Navy has been installing physical barriers on top of toxic soil instead of removing contamination, according to the watchdog group’s analysis of 33 public Navy documents cited in its report. The Navy says it is depending on these “durable covers” to protect future residents.

In many cases, the covers are a thin layer of clean soil or asphalt. Existing sidewalks, roads and building foundations also are considered to be “covers.”

“The public thinks the site is going to be cleaned up. It’s not,” said Daniel Hirsch, retired director of the environmental and nuclear policy program at UC Santa Cruz and the watchdog group’s president.

The shipyard cleanup is currently on hold and homebuilding there mostly stalled after a data-faking scandal plunged the redevelopment project into uncertainty. Before any new pieces of land can be developed, they must be retested for contamination. Once the retesting is complete, the Navy plans to move forward and transfer pieces of land to the city for development. On large swaths of that land, contamination will be left in place beneath covers, according to the report.

For the past four years, the watchdog group has been scrutinizing the troubled cleanup of the former shipyard, the largest and most complex Navy Superfund cleanup in the country: 900 acres of fields, broken-down buildings and water along the city’s southeast waterfront. It is located in the Bayview-Hunters Point neighborhood — a community of color where people are poorer and sicker than their counterparts in the city’s wealthier enclaves.

The shift in cleanup strategy has attracted little attention, despite being outlined in Navy reports mandated by federal Superfund law. One reason may be that the Navy often communicates in technical jargon, scattering key details of its plans throughout lengthy documents that can be difficult to understand. Meanwhile, some city officials have continued to claim that the shipyard will be returned to its “natural state,” though that is no longer the plan.

In fact, the city and other shipyard regulators, including the U.S. Environmental Protection Agency, have allowed the use of soil covers in recent years.

A city health department spokeswoman emphasized that the covers had been discussed at public meetings, but she did not immediately respond to the Committee to Bridge the Gap’s report. The shipyard developer also did not immediately respond. The EPA declined to comment.

The Navy says the covers are effective and that people who may live on top of them will be safe. The covers, it says, are designed to protect residents against naturally occurring metals and asbestos in the soil below. Because contamination still exists beneath the covers, the Navy attaches restrictions to the land, prohibiting “land disturbing activity.” Similar types of covers and restrictions have been implemented at brownfield sites elsewhere in the Bay Area, including at Mission Bay and Emeryville.

“To ensure that the covers remain protective, the Navy monitors and maintains these covers through regular inspections of pavement conditions, cracks in building foundations, settlement, and accumulation of surface water, the condition of survey benchmarks and signs of vandalism,” the Navy said in a statement.

But the new report by the committee, titled “From Cleanup to Coverup,” argues that covers have failed at other sites around the country and could easily be breached by plant roots, animals or erosion, bringing toxins to the surface. The report also points out that regulators have disputed the Navy’s contention that soil toxins are naturally occurring, and that industrial chemicals, heavy metals and radioactivity still linger at the site. And the report argues that future home construction projects will necessarily damage the barriers, making the rules against disturbing soil “pure fiction.”

The group spent the last year poring over the Navy’s records to trace this fundamental change in San Francisco’s most ambitious redevelopment project since the 1906 earthquake.

In the late 1990s, when the effort to scour the derelict shipyard began in earnest, the Navy decided it would clean the site to the strictest standards and give the land to the city for “unrestricted” residential use, Navy reports show. This meant that by the time the cleanup of any area was finished, any remaining toxins would be minimal, and people living there could plant tomatoes or dig in the soil without worrying about contamination.

That approach, however, was based on a flawed assumption: that contamination would be sporadic, mostly confined to the sites of known historical spills, according to the committee’s report.

The first piece of land transferred to the city, a 75-acre hilltop region known as Parcel A, was not tested for radioactivity. The Navy and regulators argued that the land had mostly been used for officer housing and there was no reason to suspect contamination there. Parcel A was given to the city without restrictions in 2004. It is now a residential neighborhood of homes and parks.

The next piece of land tackled by the Navy, Parcel B, lay downhill from there. At first, the Navy planned to apply the most rigorous cleanup standards to the parcel. But in the late 1990s, cleanup crews discovered dramatically more toxic material than expected, and work was suspended twice in the next several years.

Around the same time, a landfill along the shipyard’s western border caught fire and smoldered for weeks before the Navy notified the EPA and city. The fire on the heavily tainted site and the secrecy around it infuriated many in Bayview-Hunters Point, where residents have high rates of cancer and respiratory diseases.

In 2000, Bayview residents demanded that the Navy clean the shipyard to the strictest standards. Federal law says that owners of Superfund sites — in this case, the Navy — and the EPA must take into account the wishes of the surrounding community. Seizing on that fact, city supervisors crafted a ballot measure dubbed Proposition P.

“The Navy plans to leave behind so much contamination that it will increase the risk for cancer resulting from exposure to the property, requiring the construction of barriers and the restriction of future land uses,” the text of the proposition read. It specifically rejected physical barriers like durable covers, calling for the Navy to “clean the Shipyard to a level that will enable unrestricted use.”

Prop. P passed on the November 2000 ballot with 86 percent of the vote; the Board of Supervisors adopted it as official city policy the following year. “If the Shipyard is not adequately remediated,” the board’s resolution said, “thousands of residents, tenants, workers, visitors and neighbors will be exposed to residual toxic hazards from an incomplete cleanup.” Then-Supervisors Gavin Newsom and Mark Leno and current Supervisor Aaron Peskin, among others, supported it, and then-Mayor Willie Brown signed it.

A full, no-compromises cleanup of the shipyard was now official city policy. But in the years that followed, city leaders seemed to ignore it.

“The policy didn’t change; the policy remained in effect,” Hirsch said. “They simply began to violate the policy.”

In 2006, when it looked like the San Francisco 49ers might leave the city, Newsom, who was then mayor, and his aides tried to keep them by proposing to build a new football stadium on the Superfund site. To meet the team’s deadlines, the Newsom administration wanted to accelerate the transfer of shipyard land, focusing on a subset of cleanup tasks and leaving the rest for later.

In a February 2007 memo to Navy, EPA and state regulators, the mayor’s base redevelopment guru at the time, Michael Cohen, argued that existing cleanup policies posed “unreasonable burdens on development.” Cohen added that it was time for “a fresh re-evaluation” of cleanup standards and that a “cover remedy” made sense.

Meanwhile, the city’s Department of Public Health discussed how it might support the new direction. In a stunning memo created on a health department computer in June 2007, an official proposed “to stall some clean[up] efforts in order to kick start the redevelopment in a few small areas.”

The city memo, obtained by The Chronicle through a public records request, was headlined “NOT FOR DISTRIBUTION — BRAINSTORMING DOCUMENT ONLY — EXPLORATION OF ANY IDEA — EVEN IF OUR AGENCIES COULD NOT SUPPORT IT.” The memo acknowledged that for a public health agency to promote development at a Superfund site would be unorthodox — “seemingly contrary to the traditional public health and environmental” goals of the agency. Still, delaying the cleanup “in favor of short term redevelopment can be viewed as enhancing public health,” the health official argued, “because of the generation of jobs, housing and other opportunities that allow for improvement in quality of life.”

It is not clear who created or received the memo. City health department spokeswoman Rachael Kagan did not respond to questions about why the department seemingly ignored Proposition P and allowed covers in subsequent years. In a statement about the memo, she said the department “has never changed its priorities.”

“That document was created in reference to the stadium development which did not get built,” she added.

The stadium plan was eventually dropped when the 49ers decided to relocate to Santa Clara. Still, San Francisco kept pushing for an accelerated cleanup, and the Navy officially reversed its earlier decision to aim for the highest cleanup standards, planning instead to place “durable covers” atop contaminated soil.

According to Navy documents, a cover can consist of two to three feet of clean topsoil, four inches of asphalt or existing infrastructure like sidewalks and roads, which are repaired to increase their durability. In a few parts of the site, covers also include a layer of “geosynthetic” material — a plastic sheet often used by civil engineers to stabilize terrain — beneath the soil or asphalt.

The report released Tuesday by the watchdog group details how the physical covers can fail. It includes articles by two former federal scientists that call the Navy’s covers limited and flawed.

William Bianchi, a retired soil physicist with the U.S. Department of Agriculture, wrote that the roots of common garden plants stretch deeper than the cover’s shallow layer of soil, and plants may absorb radioactive substances through their roots and leaves. “Radioactivity and toxic chemicals can accumulate in the plant body, leading to contaminated vegetables being ingested by the public,” he wrote.

A second expert, Howard Wilshire, a retired senior geologist with the U.S. Geological Survey, pointed out that the shipyard lies between two major fault lines, the San Andreas and the Hayward. In a major Bay Area earthquake, soil at Hunters Point might liquefy, which “could very well expose contaminated soils beneath the thin soil cover,” Wilshire wrote.

The California Department of Fish and Wildlife also has criticized the Navy’s covers in the past, writing in 2013 and in 2018 that they can easily fail. A few feet of soil, in some cases accompanied by a thin layer of plastic, isn’t enough to “prevent burrowing animals from breaching the cover and exposing the remaining contaminants” to adults or children, the agency stated.

A 1998 study of 101 buried waste sites across the U.S. found that 87 percent had existing or potential problems with contamination being spread by plants or animals. At a shuttered nuclear weapons plant in Hanford, Wash., burrowing animals were “the most likely explanation for the frequent and widespread discovery of radiological contamination on surface soils.”

Despite the 2001 city policy against taking possession of contaminated shipyard land, the San Francisco health department did not object to the Navy’s use of covers, according to the report. City officials, though, continued to tell the public that the shipyard was being fully cleaned.

In slides recently prepared for a city presentation to Bayview-Hunters Point residents, the health department wrote that the goal of the shipyard cleanup “is to bring soil and water back to its natural state.”

“The Navy’s approach, parcel after parcel, is to cover up contamination that exists at levels many times its remediation goals,” the Commitee to Bridge the Gap authors wrote in the new report. “The City well knows this and has acquiesced to it.”

Along with Hirsch, the report was researched and written by several current and former students at UC Santa Cruz. Four are co-authors: Maria Caine, Taylor Altenbern, Haakon Williams and Audrey Ford.

In three previous reports, released last year, the watchdog group argued that the Navy was botching the cleanup project in multiple ways, declaring suspect land to be clean and applying obsolete health and safety standards dating as far back as the 1970s.

Responding to the previous critiques, the Navy has defended its efforts, saying that “recent reports from outside groups” did not “provide any new factual evidence” to challenge its conclusions.

“The Navy’s first priority” at the shipyard, it wrote, “is human health and safety.”

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