The story published by the Bee on May 27 reported that the paper had found records of an apparent defect in the foundation of the span's signature tower.
Caltrans was cited in the article as defending the foundation's ability to perform as designed, but the article cited anonymous sources suggesting the opposite.
Saturday, Caltrans released a statement calling for the Bee to retract the story, which it said made false claims about the bridge, and emphasizing that the bridge meets or exceeds safety standards.
"Every concrete pile in the new bridge's tower foundation has passed three rigorous, mandatory safety tests," Caltrans director Malcom Dougherty wrote in the statement. "Every aspect of the bridge has been tested, checked and rechecked multiple times."
According to a letter Dougherty sent to the Bee's editor, Joyce Terhaar, information supporting the bridge foundation's integrity was provided to the Bee's reporter but was omitted from the story.
"The safety of millions is dependent on the engineering work we do on structures like the Bay Bridge," Dougherty wrote. "Caltrans is not beyond criticism ... but we ask that you understand your unique responsibilities to paint a fair picture of our work."
The Sacramento Bee reported on Saturday that executive editor and senior vice president Joyce Terhaar issued a statement in response claiming Caltrans had not been specific with their objections to the newspaper's story.
"We asked Caltrans officials to talk to us to explain their objections, on the record, and they rejected our request," Terhaar stated.