The Securities and Exchange Commission's civil lawsuit, filed in federal district court in Los Angeles, also accuses Mozilo of illegal insider trading.
Countrywide was a major player in the subprime mortgage market, the collapse of which in 2007 touched off the financial crisis that has gripped the U.S. and global economies.
Mozilo, 70, is the most high-profile individual to face formal charges from the federal government in the aftermath of the crisis.
Mozilo has denied any wrongdoing. His attorney did not immediately return an e-mail message for comment Thursday afternoon.
Civil fraud charges also were filed against Countrywide's former chief operating officer David Sambol, 49, and ex-chief financial officer Eric Sieracki, 52.
The trio "deliberately misled" Countrywide shareholders, SEC enforcement director Robert Khuzami said at a news conference at agency headquarters. While they painted a picture of robust performance, the real Countrywide was "buckling under the weight" of soured mortgage loans, he added.