The federal government's maintenance of the Mothball Fleet anchored off Benicia is in violation of clean water and hazardous waste laws, a federal judge has ruled.

The ruling by U.S. District Judge Garland Burrell, made public late Thursday, was a victory for environmental groups and state regulators who sued to get the ships cleaned up. More than 20 tons of paint containing lead, chromium and other heavy metals have flaked off the ships and into Suisun Bay, a key habitat for fish and birds.

"The federal government has been operating an illegal hazardous waste facility in San Francisco Bay for years," said Michael Wall, a lawyer for the Natural Resources Defense Council. "It's clear it has to clean this site up."

The U.S. Department of Transportation's Maritime Administration, which maintains the reserve fleet in Suisun Bay and at two other sites, could not be reached late Thursday.

Calling the ships a "dangerous and unacceptable risk to the surrounding marine environment," Transportation Secretary Ray LaHood two weeks ago announced the government had signed contracts to clean up and remove three ships. Two ships were removed late last year. More than 50 remain.

Wall said environmentalists would press for a rapid, enforceable cleanup schedule when a trial on remedies begins in June.

"The federal government has known about this problem since the 1990s," Wall said.

"Until trial was imminent they didn't do anything about it."

The pollution problems at the fleet came to light in 2007 when the Contra Costa Times investigated an internal report showing that more than 20 tons of paint containing concentrations of metals that qualified as hazardous waste had fallen from the ships.

Mike Taugher covers the environment. Contact him at 925-943-8257.