OAKLAND (KCBS) – Despite plenty of problems, from broken bolts to water leaks, the main contractor on the new Bay Bridge has received nearly $49 million in bonuses.

The bonuses include $20 million paid by the state to American Bridge/Fluor Enterprises for completing the job on time. This comes as questions remain about who should pay to fix problems when dozens of bolts snapped last year, and how to fix the problem of rainwater leaking into the bridge’s steel support structure.

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Officials are still trying to figure out who will pick up the $30 million tab needed to fix the bolt problem, while Caltrans is spending another $10 million to tests the rest of the bolts and metal rods on the bridge.

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There are different agencies, including the Metropolitan Transportation Commission and Caltrans, who are involved in the process. While one of the goals was to have the bridge open on time and have it be safe to use, much of the bill could be inherited by taxpayers and toll payers, including maintenance costs still to come.

Caltrans, for its part, said paying the bonuses was better than having to fight with contractors over claims the agency contributed to the delays.

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You can hear Phil Matier’s comments Monday through Friday at 7:50am and 5:50pm on KCBS All News 740AM and 106.9FM.