BOSTON – The president and founder of a former Falmouth mortgage company has been charged with defrauding the Government National Mortgage Association out of nearly $3 million.

Robert Pena, 67, was charged Thursday in U.S. District Court in Boston.

Pena, the president and founder of the now-defunct mortgage company, Mortgage Security, Inc. (MSI), was indicted on conspiracy and wire fraud charges.

He was arrested today and will appear in before U.S. District Court Magistrate Judge Marianne B. Bowler this afternoon.

U.S Attorney Carmen Ortiz said the charges arise out of Pena’s alleged scheme to defraud Ginnie Mae, the government-run corporation which makes housing more affordable by injecting capital into the U.S. housing market.

According to the U.S Attorney, Ginnie Mae guarantees the timely payment of principal and interest to investors in bonds backed by government-sponsored mortgage loans.

Pena’s company was responsible for servicing the loans in the pools it created, including collecting principal and interest payments, and placing those funds into accounts held in trust by Ginnie Mae, which would ultimately pass them along to investors.

According to the indictment, beginning in 2011, Pena began diverting money that borrowers were sending to MSI....