A Sacramento judge ruled Wednesday that the state agency charged with building a high-speed rail line from San Francisco to Los Angeles must rewrite portions of its environmental review, a ruling that could delay the $40 billion project.

Sacramento Superior Court Judge Michael Kenny issued a ruling Wednesday stating that the rail authority's voluminous Environmental Impact Report inadequately described the project and failed to address Union Pacific's refusal to share its right-of-way with the new rail system.

The judgment was prompted by a lawsuit by the cities of Atherton and Menlo Park and a coalition of environmental and transportation groups, who contended that the rail authority failed to consider the environmental impacts of running the high-speed trains through the Pacheco Pass, along the Caltrain corridor.

Kenny upheld the coalition's claim that the project was inadequately described in the environmental review.

He criticized the authority's "inadequate" description of the alignment of the high-speed rail tracks between San Jose and Gilroy.

"The lack of specificity in turn results in an inadequate discussion of the impacts of the Pacheco alignment alternative on surrounding businesses and residences which may be displaced, construction impacts on the Monterey Highway, and impacts on Union Pacific's use of its right-of-way and spurs and consequently its freight operations," Kenny wrote.

But he ruled that the rail authority fairly considered the Altamont Pass and other alignments before choosing the Pacheco Pass as its preferred alternative. The environmental review, Kenny wrote, accurately described the challenges of using the Altamont Pass.

"Substantial evidence supports the FPEIR's (final program environmental impact report's) discussion of operational and environmental issues related to the Altamont Pass alternatives," Kenny wrote.

But Kenny ruled the rail authority failed to sufficiently consider Union Pacific's opposition to the rail authority's plans. Under the agency's preferred route, Union Pacific would have to share its right-of-way with the new system.

"If Union Pacific will not allow the Authority to use its right-of-way, it appears it will be necessary for the Authority to obtain additional right-of-way outside of this area, requiring the taking of property and displacement of residents and businesses," Kenny wrote.

"However, none of this was addressed in the EIR."

Palo Alto had also filed a "friend of the court" brief in support of the plaintiffs, though the court disregarded the brief in forming its opinion.

The coalition's lawsuit maintains that the rail authority inadequately considered the merits of the Pacheco Pass and the Altamont Pass (which runs through the East Bay) before selecting the Pacheco Pass as its preferred alternative.

The plaintiffs also argued that the rail authority failed to address how it would mitigate some of the project's environmental impacts and failed to respond to some of the comments submitted by various agencies before the review was finalized.

The authority has been negotiating with Union Pacific in recent months in hopes of resolving the dispute.

Rod Diridon, a member of the rail authority's Board of Directors, said the judge's ruling doesn't necessarily mean the project will be delayed. The only part of the environmental document that would need to be restudied is the one dealing with the rail segment between San Jose and Gilroy, he said.

Diridon said the Attorney General's office was studying the judge's ruling Wednesday afternoon to determine its impacts. He also said the impact of Kenny's judgment won't be known until the judge rules on the remedial actions the rail authority must take.

"It's too early to know for sure to know what's going to happen," Diridon said.

One such action could be further negotiations with Union Pacific, Diridon said.

Elizabeth Alexis, chair of Civic Affairs for the Greenmeadow Community Association in Palo Alto, said the ruling vindicates her belief in the legal and environmental-review system.

"It's good to see that the legal system can work and that the safeguards built into the environmental review process actually work -- that a project just can't be steamrolled through," she said. "Hopefully, the High Speed Rail Authority will step back and ask, 'Is this really how we want to do this?'

"It will be a test of the rail authority's willingness to do it right. This is a 100-year project and it should be done right," Alexis said.

David Schunbrunn of the Transportation Solutions Defense and Education Fund, one of the six plaintiffs in the lawsuit challenge, told the Weekly that the ruling has an extra sweetness beyond the legal issues.

"It's particularly delicious in light of (Quentin) Kopp's blustering about this being a frivolous case last week in the San Mateo County Times," he said.

Related stories:

■ Text of judge's high-speed-rail ruling (PDF)

■ Menlo Park, Atherton join suit against high-speed rail