The plant has been shuttered since last January because of radioactive leaks from the steam generator tubes.
An official with the company denied that it misled regulators.
Pete Dietrich, senior vice president and chief nuclear officer, said in a statement that the company "would never, and did not, install steam generators that it believed would impact public safety or impair reliability.”
Boxer also chided the Nuclear Regulatory Commission's oversight of the issue.
"I don't appreciate the way this has been handled," she told reporters on Tuesday.
Now, Boxer wants the Justice Department to investigate whether the company lied to federal regulators, which could be a felony.
She is also pushing for the plant to undergo a full licensing process and public hearing before resumption of operations.
The San Onofre site is located near a fault line and near crowded regions of Southern California.
"This is nuclear energy, this is very important," Boxer said. "Look what happened at Fukishima. We have to make sure we do it right."