Caltrans will spend an additional $5.5 million to keep federally protected birds away from its construction site on the Highway 101 bridge over the Petaluma River.

The California Transportation Commission last week approved the amount, acknowledging for the first time the extent of the project’s budget overrun due to measures taken to date — and those that will be needed going forward — to assure birds are not harmed by construction.

The allocation comes as construction crews are busy preparing to demolish a part of the old highway bridge before the migratory cliff swallows return next month from their winter grounds in South America.

The birds for years have made their conical mud nests under the Petaluma River Bridge, which consists of two 907-foot parallel spans. When Caltrans in 2013 embarked on a $130 million project to replace the structure with a wider, six-lane bridge, workers installed nets under the two existing spans to keep the birds from nesting. The nets actually trapped and killed dozens of birds, prompting a lawsuit from a coalition of wildlife advocates.

As part of a settlement agreement, Caltrans took down the nets during the 2014 nesting season and replaced them with hard plastic siding that discourages nesting under the bridge. Caltrans also agreed to pay for biologists to monitor the work site and ensure bird safety, and agreed to demolish the old bridge outside of nesting season, which runs from Feb. 15 to Aug. 15.

The additional expenditures for bird monitoring, legal fees and staff time dealing with the bird issue, including public outreach, raised some eyebrows with the Transportation Commission.

“We could have built condos with that money for those birds,” said Vice-Chairwoman Lucetta Dunn.

Wildlife advocates say that the bird safety measures Caltrans implemented last season, at a cost of $4 million, have worked, but some also questioned the price tag for the efforts going forward.

“I’m very skeptical that it should cost $5.5 million to exclude birds from a bridge. That’s ridiculous,” said Jeff Miller, a conservation advocate with the Center for Biological Diversity.

“Overruns are part of how Caltrans does business. If they had done the project right in the first place, it would have saved millions in tax payer money,” Miller said. “I hope no one is going to scapegoat the birds.”

Other plaintiffs in the lawsuit against Caltrans included local Audubon Society chapters and Veronica Bowers, who runs a songbird rescue center in Sebastopol.

Caltrans spokesman Allyn Amsk said the additional funding request was what was required to complete the project given the measures needed to protect birds.

“The additional funding will allow us to complete the project in 2016 and further protect the ecology at the construction site at the Petaluma River in Sonoma County, including migratory birds like cliff swallows,” he said.

Cliff swallows are protected under the federal Migratory Bird Treaty Act. C.C. Myers, Inc., the contractor that installed the nets two years ago, was fined $3,525 by the U.S. Fish and Wildlife Service for harming the swallows. Caltrans said 67 birds died in the netting.

The bridge project is part of the $1.2 billion effort to widen Highway 101 to six lanes and alleviate congestion from Windsor to Novato. Crews are building a new six-lane bridge over the Petaluma River in the exact footprint of the 60-year-old span, a complicated feat of engineering that entails phased construction in order to keep traffic flowing.

Northbound traffic is currently being routed onto the median between the twin spans while workers demolish the old northbound bridge. The last section of bridge is slated for removal on Feb. 8, a week before bird nesting season begins. The demolition work will close Petaluma Boulevard South under the bridge for most of the day and involve a detour.

“We want to have these activities done before the start of migratory bird season,” Amsk said.

The overall project, planned for completion in August 2016, is six months behind schedule because of what Caltrans says are delays due to the bird settlement agreement.

Susan Kirks of the Madrone Audubon Society, one of the groups that sued Caltrans, said her organization would monitor the work site over the next two nesting seasons and report any violations. She said she hopes Caltrans learns from the experience and will implement the new bird safety measures on future projects.

“This didn’t happen because of the birds. It happened because of Caltrans’ egregious use of cheap netting,” she said. “Hopefully this will raise awareness and prevent future expensive tragedies and deaths. We hope for a positive outcome in the end.”