According to the San Francisco Chronicle, a CalTrans analysis shows the new span is $35 million in the red.
Until recently, officials were optimistic the bridge would cost less than the $6.4 billion originally budgeted.
There is at least $110 million worth of unbudgeted work that still needs to be done.
There are $45 million of which will come from retrofit projects on the Antioch and Dumbarton bridges.
Officials say the overruns will not lead to a toll hike.