Citing unnamed government officials with knowledge of the case, the Times said the investigation into whether Countrywide misrepresented its financial condition and the soundness of its loans in securities filings was at an early stage and it was not clear if any charges would result.
A Countrywide spokeswoman, Susan Martin, told the newspaper that "we are not aware of any such investigation." The probe was first reported on Saturday in The Wall Street Journal.
The Countrywide inquiry follows a broader investigation by the FBI into 14 companies as part of a review of the practices of the mortgage industry, the Times said.
Investigators had been looking at possible accounting fraud or insider trading connected to loans made to borrowers with subprime credit, the Times said.
Countrywide already faces federal and state investigations of its lending practices, as well as several lawsuits by investors and mortgage holders.
The Securities and Exchange Commission is conducting about three dozen civil investigations into how subprime loans were made and how securities were valued, the Times said.
State investigations include one by the Illinois attorney general, who earlier this month subpoenaed units of Countrywide Financial and Wells Fargo & Co in a probe of whether the companies violated federal lending and civil rights laws by steering minority borrowers into more expensive loans.
In that probe, Countrywide said it would fully cooperate with authorities.
Countrywide, drowning in a pool of bad home loans, is in the process of being acquired by Bank of America for about $4 billion. It reported a loss of about $422 million in the fourth quarter of 2007.