Just as the troubled $6.6 billion Bay Bridge project is wrapping up, bridge officials learned Thursday about a new dispute that threatens to dash hopes to avoid further cost overruns on the troubled project.

At a bridge oversight panel meeting Thursday, Caltrans officials outlined an emerging dispute over the $11 million tab the U.S. Navy claims Caltrans should pay to clean up what had been its landfill site on Yerba Buena Island. That site was turned over to Caltrans to allow for bridge construction back in 2001 – without the Navy doing the promised cleanup.

The Navy now asserts those cleanup costs should be footed by Caltrans because the so-called Site 11 has since been contaminated by bridge paint, waste and debris. That claim left bridge officials fuming.

“We’re not going to pay a dime to clean up the Navy’s mess,” said Steve Heminger, Executive Director of the Metropolitan Transportation Commission, after being briefed on the issue. “I just think that’s outrageous.”

Heminger, who chairs the three member bridge project oversight panel, said the demand was especially galling given the Navy’s role in fighting the planned alignment of the new span in the early days, which he says contributed to delays in construction.

“It’s outrageous that they would even ask the department after all the trouble that they caused on this project,” he said, still miffed over the Navy’s claims about shadows being cast by the span on its historic buildings.

“They created all these fictions that we were somehow going to destroy the historic structures that were out there – we of course didn’t destroy a thing,” Heminger said. “The bridge got a little closer in the air to one of the buildings out there --that’s all.”

A spokesman for the Navy did not return calls seeking comment.

Meanwhile, the oversight panel voted Thursday to settle a long-running dispute with the main contractor on the project, American Bridge/Fluor.

Under the deal, the bridge builder will get $25 million -- half has much as it had sought in its claims against Caltrans. But Caltrans will not pursue $8 million it had argued the company owed to fix the high strength rods that failed on the span back in 2013.

Caltrans is now promising to pay its $8 million share of the of the $24 million bill for the retrofit of the broken rods and has pledged to press bridge consultants TY Lin International to pay their one-third share of the fix.

That sum could help bring in the seismic retrofit program without a deficit, or even with a surplus, thanks to $24 million in savings from other bridge projects.