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SACRAMENTO – Strengthening the state’s toll bridges against earthquakes, a job already costing twice initial 1990s estimates, could rise another $630 million and imperil other transportation projects, a new state audit warns. 

The audit, released Thursday, chronicles how a $2.2 billion project to retrofit seven major bridges by 2004 has turned into a $4.6 billion project that will take until 2009. Most of the cost overruns and delays stem from a single development – a $1.3 billion “signature” upgrade for the Bay Bridge’s new eastern span. 

Bay Area bridge tolls doubled in 1998 from $1 to $2 to pay for the upgrade, and will continue to 2038, long beyond their original 2008 expiration date. 

State auditors drew no conclusions and made no recommendations in the report. But they expressed fears that still more cost overruns between now and 2009 could add $250 million to $630 million to the job and stall other transportation projects in California. 

“It’s a bit of a warning,” said Steven M. Hendrickson, chief deputy state auditor. “These costs could go up further.” 

Caltrans officials responded to auditors’ alarm, promising cost-saving measures to stay within the project’s current budget. 

But Hendrickson said, “We would remain skeptical.” 

The audit proves one of the oldest adages about large government construction projects: things typically cost more money and take more time. Disputes, delays and design changes have also added millions in cost overruns for staff salaries, consulting fees, concrete and steel. 

Caltrans Chief Jeff Morales, in a letter responding to the audit earlier this month, cited complexities of estimating retrofit costs for the “most challenging major bridge projects in the world.” He wrote, “While the Department has drawn upon world-renowned expertise in the development of the project, much of the work has no historical precedent.” 

Retrofitting the seven state-owned toll bridges is occurring alongside a separate $2.5 billion effort that has already shored up more than 2,000 highway bridges against a major earthquake. Likewise, Caltrans has finished retrofitting the Vincent Thomas Bridge in San Pedro, the San Diego-Coronado Bridge and the Bay Area’s Benicia-Martinez, Carquinez and San Mateo-Hayward bridges. 

The audit notes that delays especially plagued the Carquinez Bridge project. The Southern Pacific Railroad bought the Union Pacific Railroad while Caltrans negotiated over relocating its tracks. The relocation took 143 days longer than expected, while moving a gas line from one side of the bridge to the other took 87 days longer than PG&E originally promised. The audit also recounted a two-year delay with the Bay Bridge’s new eastern span as Caltrans ran into environmental and alignment disputes with the U.S. Navy and Army Corps of Engineers. The Richmond-San Rafael Bridge retrofit also remains unfinished. 

“With something this complex, for some things that are really massive public works projects, it’s inevitable there are going to be changes in costs,” said Brenda Kahn, spokeswoman for the Bay Area’s nine-county Metropolitan Transportation Commission. 

The U.S. Geological Survey estimates a 70 percent chance of a 6.7 magnitude earthquake in the Bay Area by 2030.