The U.S. Navy knew as far back as 1993 that the tap water at its former shipyard in San Francisco contained dangerous amounts of lead, but didn’t tell local officials, visitors or people who worked there, including hundreds of police employees stationed at the site since 1997.

Documents obtained by The Chronicle show how the Navy has sometimes kept other government agencies and the public in the dark about hazards at the old Hunters Point Naval Shipyard, a sprawling Superfund waste site contaminated with radioactivity and industrial pollutants.

For the past quarter century, the Navy has hired contractors to remove or cover toxic material and prepare the 500-acre site for transfer to San Francisco, which plans to turn the land into homes and businesses. But the cleanup has been roiled by a scandal over faked soil data and allegations of wider fraud. A recent Chronicle investigation revealed that shipyard dangers weren’t properly explained to the San Francisco police employees who worked there for years, according to interviews with dozens of retired officers and communications and documents from that time.

House Minority Leader Nancy Pelosi has called for a federal investigation into the Navy’s main shipyard cleanup contractor, Tetra Tech, as well as the potential failings of the Navy and the U.S. Environmental Protection Agency, citing an “unacceptable cloud of fear and doubt” and a “disturbing lack of transparency.”

“Who knew what, when?” Pelosi asked Tuesday.

Tetra Tech has stood by its work and has said that any wrongdoing was confined to a “cabal” of rogue employees. The Navy owns the shipyard, and the U.S. Environmental Protection Agency regulates its cleanup. Both have defended their oversight of the former base.

The new documents reveal a piece of what the Navy knew during an early, formative phase of the cleanup.

In 1993, Navy tests concluded that the drinking water supplied to shipyard buildings was contaminated with lead and copper, probably from corrosion in the pipes. The amount of lead in drinking-water samples was “significantly” above safe levels, a Navy official wrote years later in a letter to the San Francisco’s development agency.

Lead can cause cancer and brain damage and is particularly poisonous to pregnant women and children. One water sample tested by the Navy contained 15 times the safe amount of lead.

Copper also showed up in the drinking-water samples, though at levels considered acceptable by the EPA. Copper is potentially harmful to the blood, liver and kidneys.

More Information Dangerous Ground Read The Chronicle’s investigative reporting on the former Hunters Point Naval Shipyard and related issues online: www.sfchronicle.com/dangerous-ground Email The Chronicle’s Investigative Team: iteam@sfchronicle.com To learn how to contact reporters confidentially: https://projects.sfchronicle.com/newstips/

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Despite learning that the shipyard’s water was dangerous in 1993, the Navy didn’t disclose the information right away.

In 1996, the Navy leased three shipyard buildings to the city. One of them, known as Building 606, became the new home for specialized police units such as the SWAT Team, the dirt-bike unit, the K-9 unit the Muni Transit unit and the citywide crime lab. Yet the Navy didn’t mention the water contamination in lease paperwork for Building 606. It offered the building “as is,” and the city signed on without performing its own tests of the water.

Police employees, both officers and civilians, started transferring to Building 606 in February 1997. By March, about 40 police officers were working there. Early on, they drank the tap water and also used it to take showers and brush their teeth, according to interviews with 30 former officers who were stationed at the building.

It wasn’t until that summer when the Navy finally issued an alert.

Hunters Point Shipyard “is concerned with the quality of the drinking water provided to employees, tenants, and visitors on the station,” Navy base-closure official Beverly Freitas wrote to the city’s development agency on July 16, 1997, detailing the troubling lead results from 1993.

Appearing surprised, city official June Bartholomew replied in a letter on Aug. 13, The city had “significant questions and concerns about the limited information you provided,” she wrote, then posed nine sharp questions to the Navy, among them: “Why the delay in notification to the [city]?” and “What specific steps will the Navy take to address the long term lead problem?”

The development agency, which provided the Navy’s letter to The Chronicle in response to a public records request, said it had no record of a reply to Bartholomew’s letter.

At some point during 1997, police employees working at Building 606 were told by commanders to stop drinking the tap water, officers who worked there recalled. They were also told that showers and brushing teeth were fine. The Police Department brought in bottled water.

The Navy did not immediately respond to a request for comment. A San Francisco Department of Public Health spokeswoman referred to previous assurances the department has given about the safety of Building 606’s water. A department of health industrial hygienist said in 1999 that that she believed the water issues were resolved by “flushing” the pipes. Both the health department and the Navy have maintained that any potential hazards were properly addressed and that the police building, and the people within it, are safe.

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