The indictment also named Morgan's son, Todd Morgan, and two other principals of his Pittsford-based Morgan Management, LLC.
The Morgans, along with broker Frank Giacobbe and former finance director Michael Tremiti, pleaded not guilty Wednesday.
"Today's charges allege Robert Morgan and the men he surrounded himself with in business worked hard with the desire to creatively subvert the integrity of the financial industry," FBI Special Agent-in-Charge Gary Loeffert said at a news conference.
The indictment seeks the forfeiture of $267.3 million and multiple apartment complexes in Rochester, Buffalo and elsewhere in upstate New York and Pennsylvania.
The charges come a year after the indictments of three other company principals, who have since pleaded guilty. Authorities said the investigation is ongoing.
According to his website, Morgan's portfolio contains more than 140 properties and 34,000 units in 14 states.
Prosecutors said the company provided false information about the income of properties in several states to secure loans from institutions including the government-controlled Freddie Mac and Fannie Mae. Managers kept two sets of books for at least 70 properties, investigators said - one showing accurate figures and the other filled with manipulated numbers given to lenders for servicing and refinancing loans.
"The scope of the dishonesty and the deceit alleged here, both in the geographic sense as well as in a dollar amount, of the mortgages and properties involved is very expansive," U.S. Attorney James Kennedy Jr. said. "This type of fraud strikes at the very heart of those banking, insurance and mortgage industries."
Charges against the men include conspiracy to commit wire fraud, bank fraud and money laundering. The Morgans also are charged in a $3 million insurance fraud scheme for allegedly inflating repair invoices on claims submitted to insurers.
Robert Morgan's attorney could not be reached by phone after the indictments were announced. Todd Morgan's attorney, David Rothenberg, and Tremiti's attorney, Donald Thompson, declined to comment. Giacobbe's attorney did not immediately return a phone message.
If convicted, the businessmen could face up to 30 years in prison.
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