The agency charged with building California's high-speed rail system adopted a crucial environmental document for the rail line Thursday morning, despite calls from Peninsula critics that the new document is deeply flawed and could lead to litigation.

The California High-Speed Rail Authority had initially certified its program environmental impact report (EIR) for the Bay Area-to-Central Valley section of the voter-approved line in 2008. The agency was forced to de-certify and revise the document last year because of a court order prompted by a lawsuit from Menlo Park, Atherton and a coalition of nonprofit groups.

The new document includes revisions to sections dealing with project description, vibration impacts and Union Pacific's opposition to sharing its corridor with the new high-speed-rail system. But it does nothing to dispel the concerns voiced by Peninsula cities about the ridership projections in the document.

Stuart Flashman, the attorney who represented the plaintiffs in the lawsuit against the rail authority, said the coalition was disappointed in the revised document, which he said "raises more questions than it answers." The new document, for instance, does nothing to address widespread criticism of the rail authority's ridership projections. The rail authority used these projections to justify its selection of the Pacheco Pass in the Peninsula as the preferred alternative for the rail line, as opposed to the Altamont Pass in the East Bay, which the plaintiffs supported.

In June, the Institute of Transportation Studies at U.C. Berkeley found these projections to be flawed and unreliable, echoing earlier concerns from the the Palo Alto-based group Californians Advocating Responsible Rail Design (CARRD).

Palo Alto, which had filed a motion supporting Menlo Park and Atherton's suit, also asked the rail authority to take a fresh look at its ridership projections, a request that the new document doesn't address.

Flashman told the board of directors that by failing to reconsider the ridership numbers, the rail authority is opening itself up to fresh litigation.

"If you go ahead and certify this, you'll be ending up in court again and probably facing another adverse decision, which I think will be bad for the project," Flashman said.

Atherton Councilman Jerry Carlsen echoed Flashman's sentiments and urged the rail authority not to certify the new document, which he predicted "would further deepen the distrust of the authority."

"This will certainly be an area of further litigation if the document is approved as is," Carlsen said.

Palo Alto officials, meanwhile, submitted a letter to the rail authority stating that the new document fails to address the city's comments. Rob Braulik, the city's project manager for high-speed rail, asked the board not to certify the environmental document and to reanalyze the possibility of running the rail line along Altamont Pass.

Despite these concerns, the rail authority board of directors voted Thursday morning (in the second part of a two-day meeting) to certify the environmental document. In a statement, the rail authority said it responded to more than 3,700 comments from more than 500 agencies in the new EIR.

Curt Pringle, chairman of the rail authority's board of directors, called the board's decision to certify the document "another major step forward in making California the home of the nation's first high-speed rail network."

"Californians want this project done right, and that means a careful and thoughtful assessment of how to minimize environmental impacts while building a project that creates enormous opportunity for the people of the state," Pringle said in a statement.