Three major banks have stopped offering mortgages for homes at the former Hunters Point Naval Shipyard, an extraordinary move likely to complicate the already troubled effort by the city and developers to transform 500 acres of waterfront in San Francisco.

The banks, Wells Fargo, Chase and Citi, all confirmed to The Chronicle that they are not providing loans to any buyers at the San Francisco Shipyard development at the moment. They cited reasons related to unresolved questions about the safety of the land where mega-developer Lennar Corp. has built about 450 homes and is planning thousands more.

The home area — a 75-acre hilltop site known as Parcel A — is adjacent to America’s largest Superfund site, hundreds of acres contaminated with radioactive materials spread by the Navy during the Cold War and undergoing cleanup since the early 2000s. In recent years, a scandal involving falsified radiation tests has marred the effort, raising concerns that toxic hazards were missed or covered up — and spawning lawsuits against Lennar from angry homeowners.

It is unclear how many banks may still be offering mortgages for homes on Parcel A. Lennar said in a statement that multiple banks are still lending to home buyers. But real estate and economics experts said the decision by the three banks is exceptionally rare and reflects an atmosphere of uncertainty about the shipyard and its future.

The move might affect current shipyard homeowners as well as potential buyers, they said, because if banks aren’t lending, people wanting to buy might have to pay in cash, and people wanting to sell could struggle to unload their properties.

“If you freeze financing on that — wow,” said Denis DeSaix, a real estate appraiser and incoming president of the Northern California chapter of the Appraisal Institute. Depending on the extent of any contamination and the difficulty of removing whatever hazards exist, “It could be a ghost town there for a while.”

Chris Thornberg, founding partner of Beacon Economics, an economic consulting firm based in California, said the banks’ move could cause serious ripple effects, possibly making it more difficult to pay off construction loans, upsetting the development’s investors and potentially leading to more lawsuits.

“If the banks aren’t lending to people to buy these homes, then everything else falls apart,” Thornberg said. “Basically all hell breaks loose.”

The only comparable drama to play out in San Francisco in recent years has been at Millennium Tower, a glass pillar of lavish condos that is leaning and sinking — and plunging its residents, the developer and the city into litigation. The Chronicle reported in 2016 that after writing $67 million worth of loans for condos at the tower, First Republic Bank decided to stop lending.

While all-cash transactions are common in the Bay Area’s superheated housing market, shipyard condos have been designed and pitched as a relatively affordable solution for first-time homebuyers, with some condos previously selling from around $560,000.

“We’re not talking about high-tech millionaires,” said Patrick Carlisle, chief Bay Area market analyst for Compass, a residential real estate firm. “We’re talking about people buying their first homes, or looking to stay in the city. If they can’t get a loan, it’s over. They can’t buy.”

And when large banks shut off funding, Carlisle added, other banks usually follow. “Nobody wants to be on the wrong side of a financial situation like this,” he said.

According to records from San Francisco’s Office of the Assessor-Recorder, only one housing unit sold in the hilltop area from Sept. 1 to Dec. 12. A condominium with a reported sale price of $725,000 sold in mid-September, with a mortgage provided by Quicken Loans.

Quicken Loans did not respond to a question about whether the company is still lending at the shipyard.

In response to questions from The Chronicle, Lennar said the home area at the shipyard is safe and that the company has sold and closed homes since August.

“As the facts become more widely known, we believe the lending environment will normalize and more banks will provide loans,” the company said in a statement.

Headquartered in Miami, Lennar is the nation’s largest home builder, completing almost 30,000 new homes last year and generating $12.6 billion in annual revenue. The shipyard development is an $8 billion project that has been fueled in part by EB-5 funds, a U.S. immigration program that essentially trades green cards to foreign financiers in exchange for investments that lead to jobs.

Lennar also has long-established ties to the city’s power structure. Willie Brown, the former mayor and current columnist for The Chronicle, raises money for Lennar as a principal with the EB-5 investment fund Golden Gate Global. Brown’s onetime deputy Kofi Bonner is a top executive with Lennar spin-off FivePoint Holdings.

The shipyard is the city’s largest redevelopment project in a century, part of a new bayshore community where developers have planned 12,000 homes, more than 3 million square feet of office space and 300 acres of parks. Lennar is in charge of the first phase, and FivePoint Holdings is handling the second wave, which includes homes at nearby Candlestick Point. Between the two phases, about 750 housing units have been created so far, and Lennar is currently selling a new outcropping of luxury townhomes that start at $1.4 million.

Asked if the company had ever experienced a similar situation in any of its hundreds of home communities throughout America, Lennar said in a written response: “No.”

The shipyard scandal has already taken a toll on the developers, according to city records and an interview Bonner gave to The Chronicle’s editorial board this year. By early 2017, city documents show, six buyers of Lennar homes at the shipyard had backed out of their contracts because of concerns over their health and safety.

Bonner also told the editorial board that if uncertainty about the shipyard’s future becomes too great, FivePoint could consider abandoning its plans to build homes at the shipyard and focus on developing at Candlestick Point. But he didn’t think such a step would be necessary.

“We are very excited by the prospect that this cloud will be lifted at some point — at the end of the day, uncertainty is bad for business and terrible for the people who live there,” Bonner said then.

A FivePoint spokesman did not respond to a request for comment on this story.

The Parcel A home area was transferred from the Navy to the city in 2004; multiple agencies declared it safe for development and free of harmful radioactivity. But in 2014, whistle-blowers who had worked for lead cleanup contractor Tetra Tech emerged and said that the cleanup process on the Navy-owned portions was fraudulent and broken. Two former shipyard workers also raised questions about possible contamination on Parcel A.

Since then many of the whistle-blowers’ allegations have been confirmed by government agencies. This year the Department of Justice announced that two former Tetra Tech cleanup supervisors had admitted to faking radioactivity tests to make the site appear cleaner. Tetra Tech has said that all problems were caused by a few “rogue” employees, but both the Navy and the U.S. Environmental Protection Agency have concluded that the company’s radioactivity measurements can’t be trusted and the site should be retested.

The Navy has said that may end up costing taxpayers more than a half-billion dollars and could delay the transfers of other shipyard parcels by about a decade.

Uncertainty about the extent of contamination has caused some homeowners to question the safety of the hilltop home area. The California Department of Public Health recently agreed to perform a limited search for radiation, walking across some pieces of the parcel with handheld and machine-towed detectors that can see one type of radiation but not other types.

The survey, which began in July and was completed in October, turned up a buried, highly radioactive object: a radium-filled deck marker once used by the Navy. Beyond that, the scan found nothing out of the ordinary, the state has said. But critics have said the only way to confirm the safety of the parcel is to take soil samples, as the Navy has done in other parts of the shipyard.

The state health department says the final report on its scan will be released in the next few weeks. Meanwhile, about 20 homeowners have filed lawsuits against Lennar and Tetra Tech, alleging that the companies withheld key facts about contamination at the shipyard. Lennar and Tetra Tech have said the suits are baseless.

One of the plaintiffs, Salustiano Ribeiro, said he bought a condo at the shipyard last summer and has since grown worried about his health after learning of fraud that occurred in the shipyard cleanup.

“I love the condo,” said Ribeiro, who works as a laboratory scientist. “The view is beautiful. But I don’t know if in 10 years if I’m going to develop a type of cancer that’s related to the area where I live.”

A spokesman for Wells Fargo said the bank is not lending at the shipyard because of the homeowner lawsuits against Lennar.

“Due to the nature of the pending litigation,” Tom Goyda said in a statement, “the Naval Shipyards development does not meet Wells Fargo and industry project eligibility standards and we are unable to provide mortgage loans on individual condominiums and townhomes in the development.”

According to an email that a Chase loan officer sent to Ribeiro, Chase is not lending at the shipyard because it is waiting for the state health department’s final report on the radiation scan. A Chase representative confirmed that the company has halted lending, but did not comment further.

The government-sponsored mortgage giant Fannie Mae stays away from loans for condominiums when the developer “is named as a party to pending litigation that relates to the safety, structural soundness, habitability, or functional use of the project.” Fannie Mae guarantees home loans, and many banks use the organization’s guidelines to design their own lending policies.

“In the end, it is mortgage loans that are going to cover this project,” Thornberg said. “And if those aren’t being made, then someone is going to be left holding the bag.”

The state health department has already released a letter saying that its radiation scan of the home area is complete, only the one radioactive deck marker was found, and the rest of the scanned areas appeared normal, though the agency is still reviewing the data. Lennar said it expects that when the final report is issued, the lending environment will return to normal.

Like the other agencies that perform oversight of the shipyard cleanup, the state health department did not discover problems with Tetra Tech’s work until whistle-blowers emerged in recent years. It’s unclear whether homeowners will accept the conclusions of the department’s final report on Parcel A.

“Let’s do a soil testing,” said Ribeiro, the homeowner and plaintiff against Lennar. “Let’s do a full evaluation of the soil. But they will not do it.”

Ribeiro worries that until all questions are fully answered about Parcel A and what went wrong with the wider shipyard cleanup, he will have a hard time trying to sell his home.

“I feel stuck in the moment,” he said. “I just want to get out of here.”

Chronicle staff writers J.K. Dineen, Roland Li, Kathleen Pender and Gwendolyn Wu contributed to this report.

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