"DOJ could not provide readily verifiable data related to its criminal enforcement efforts because of underreporting and misclassification of mortgage fraud cases in the case management system used by the Executive Office for United States Attorneys (EOUSA)," the report reads.
One glaring example of inaccurate reporting was cited by the OIG. Specifically, it says, the Justice Department inflated the number of criminal defendants by five-fold during an October 2012 highly publicized press conference. The event was held to tout the success of the Distressed Homeowners Initiative, a mortgage fraud program involving the Justice Department and the Financial Fraud Enforcement Task Force. It took a year for the Justice Department to correct the mistake.
(Read more: What happens to prices when Wall Street is your landlord)
The OIG did find some examples Justice-led efforts to prioritize the investigation and prosecution of mortgage fraud cases, including the Criminal Division's leadership of its mortgage fraud working group and the Federal Bureau of Investigation's (FBI) and United States Attorneys' Offices' participation on more than 90 local task forces and working groups.
Justice spokesperson Ellen Canale said: "The facts regarding the department's work on mortgage fraud tell a much different story than this report. In the time period in question, the number of mortgage fraud indictments nearly doubled, and the number of convictions rose by more than 100 percent. As the report itself notes, even at a time of constrained budget resources, the department has dedicated significant manpower and funding to combatting mortgage fraud."
UPDATED: This story was updated to include comment from the Justice Department.
—By CNBC's Diana Olick. Follow her on Twitter @Diana_Olick.