Experts who reviewed concrete and engineering records for the Sacramento Bee newspaper questioned a 19-foot section in the bridge's main tower foundation.
Records indicate the concrete in the foundation had not hardened before tests were conducted.
However, Caltrans says it believes the concrete has hardened and that the bridge can withstand any anticipated earthquake.
During the Bee's reviews, the newspaper said it also found that two of the 13 piles that rise out of the Bay to hold up the main tower were not tested properly.
Caltrans plans to open the $6.5 billion structure by Labor Day 2013 to serve an estimated 100 million drivers annually.
The Associated Press contributed to this report.