The Sacramento Bee reported that the findings have alarmed engineering experts who say the rust could have long-term implications for the new span.
Bridge spokesman Andrew Gordon told the newspaper in an email that "there is no concern" about corrosion. He attributed the rust to metal shavings and particles from grinding and other work.
"We have seen no signs of degradation of the strands or rods," Gordon said.
The $6.5 billion bridge has an unusual design: A single cable comprised of 137 steel strands loops over a tower and under the bridge to hold it up. That cable is secured inside chambers designed to keep out water and marine air to prevent corrosion.
The newspaper said rust has been found inside one of the chambers where the suspension cable is attached.
The bridge was designed to stay in use for 150 years.
Engineering experts told the newspaper the corrosion is significant because it makes the rods and the cable strands vulnerable to cracking.
If the strands crack where they are attached, continual vibration caused by trucks overhead would worsen the cracks and jeopardize the strength of the span's single main cable, said University of California, Berkeley, engineering professor Abolhassan Astaneh-Asl, a well-known expert on steel bridge engineering.
"The implications are structural and very serious," said Astaneh, referring to the lifespan of the bridge. "This bridge is fracture critical, which means if any important element of this bridge fails ... the bridge is going to collapse."
The newspaper said white and red-brown rust can be seen in patches on the threads of dozens of rods in chambers, 130 feet long and 15 feet high, on the eastern end of the bridge. Rust-encrusted cable strands at the junctions of dozens of sockets and crack-like indentations are apparent in a few cases.
Many of the rods are considered potentially vulnerable to cracking, partly because of manufacturing errors that let hydrogen enter the steel. A combination of hydrogen, rust and stress can create tiny cracks in the steel that grow and cause the rods to break.
The newspaper said experts urge the California Department of Transportation to move quickly to fix the problem.
Gordon, the bridge spokesman, noted work continues on the span.
"The opening of the bridge in September did not mean that all work was completed," he said.