A Miami federal grand jury is investigating South Florida’s preeminent affordable-housing developer, the Carlisle Development Group, on allegations that it bilked the U.S. government out of millions of dollars in tax subsidies used to finance more than a dozen rental projects in Miami-Dade and Broward counties.

Carlisle is suspected of committing fraud by padding construction costs of the rental apartments to generate higher government-issued tax credits for itself and its investors, according to sources familiar with the probe. Prosecutors are trying to prove that top executives of Carlisle, a for-profit company, worked in cahoots with a Fort Lauderdale building contractor to unlawfully pocket those extra tax credits, the sources said.

The grand jury is focusing on two of Carlisle’s chief executive officers, Matthew S. Greer and retired CEO and founder Lloyd J. Boggio, as well as a general contractor Michael K. Runyan, according to a subpoena obtained by The Miami Herald.

The subpoena, issued in January in connection with “an official criminal investigation of a suspected federal offense,” names Carlisle and its development entities, along with the three businessmen. It seeks loan and other records for two of Carlisle’s rental projects built by Runyan’s Fort Lauderdale company, BJ&K Construction Services, in the low-income Little Haiti and Allapattah neighborhoods.

Both the city and Miami-Dade governments partially financed those high-rise apartment projects, Villa Patricia and Amber Garden, with multimillion-dollar, low-interest loans.

The subpoena is a mere snapshot of the grand jury’s investigation into Miami-based Carlisle, the state’s biggest and the nation’s third-largest affordable-housing developer with more than 80 completed projects valued at $1.4 billion.

On Saturday, the company’s lawyer, former federal prosecutor Jeff Marcus, issued a statement: “Carlisle intends to cooperate fully with this investigation and looks forward to a speedy resolution so it can get back to helping provide affordable housing for Miami’s neediest. The company is proud of its track record, which includes housing over 13,000 low income residents, including working families, the elderly, youth aging out of foster care, and the formerly homeless.”

Carlisle was founded by Boggio and Greer’s father, attorney Bruce Greer, in 1997. Matthew Greer joined the development company in 2004 and rose to CEO four years later, replacing Boggio. He remained as a principal.

Carlisle has garnered kudos over the past decade — despite a rough patch in the aftermath of the nation’s 2008 financial crisis — as a socially and environmentally conscious developer.

The firm has been credited with developing attractive apartment complexes in blighted urban areas, and with improving the lives of people who could never afford market-rate rents in South Florida and elsewhere.

Carlisle’s website lists awards won by Greer, including the 2009 Urban Land Institute’s Young Leader prize and the South Florida Business Journal’s 40 under 40 recognition.

The investigation into Matthew Greer, Boggio and Runyan, the contractor, started in late 2011 when two senior Carlisle executives quit and became whistle blowers for the feds, cutting cooperation deals with the FBI, Internal Revenue Service and U.S. Attorney’s Office.