"There are no sacred cows," Barra said. "He is going to do his investigation and we will let the facts and results of his investigation drive us."
Meanwhile, the Justice Department is saying little about GM.
"I would not confirm [nor] deny the existence of any investigation, but what I would indicate is that the announcement that we are making today is reflective of the aggressive nature that we will take in looking at these kinds of charges, and also the way in which we will resolve them," Holder said.
"I think this is a sign for the industry that we take these matters seriously. Individuals and corporations will be held accountable and the great work that has been done by this team can be replicated if that is necessary."
Toyota's actions 'shameful'
Five years ago, when Toyota was in the midst of the recall crisis surrounding vehicles that may have unintentionally accelerated due to sticky gas pedals, the company reassured the public everything was OK with millions of Toyota models. In reality, the automaker wasn't telling the truth.
Holder called Toyota's handling of the unintended acceleration crisis "shameful."
"By the company's own admissions it protected its brand ahead of its own customers. This constitutes a clear and reprehensible abuse of the public trust," he said.
(Read more: Something went 'very wrong': GM CEO)
As a result, Toyota will now pay the largest ever penalty for an automaker, be put on probation for three years and have an independent monitor ensure the company is abiding by the law when alerting the public about potential safety issues.
In exchange for complying with those stipulations, the Justice Department has agreed not to file criminal charges against the automaker.
In a statement, the company said: "Toyota has cooperated with the U.S. Attorney's office in this matter for more than four years. During that time, we have made fundamental changes to become a more responsive and customer-focused organization, and we are committed to continued improvements."
—By CNBC's Phil LeBeau. Follow him on Twitter
Questions? Comments? BehindTheWheel@cnbc.com.