The Gambino crime family schemed with a union official, a developer, and an elevator company owner to over-bill the Metropolitan Transportation Authority more than $10 million for renovations to its new headquarters, prosecutors charged yesterday.

The charges unsealed in federal court in Brooklyn contain the latest accounts of alleged corruption at a project that has come in hundreds of millions of dollars over budget and spawned at least 12 arrests.

The project was designed to bring thousands of workers for the nation’s largest mass transit system together under one roof.

Costs have risen from an initial outlay of $130 million to more than $400 million, although the exact amount of the cost overrun, like much about the project, remains under dispute.

An MTA spokesman said unexpected amounts of asbestos and other problems account for a portion of the overrun.

Mario Garafola, a reputed Gambino family associate, his father Edward, an alleged Gambino soldier, and Junior Campbell, a laborers’ union business agent, were charged in an indictment that included allegations of fraud, racketeering and other crimes.

They were released on bail after their arraignment. Attorneys for Edward Garafola and Mr. Campbell did not immediately return phone calls seeking comment.

Mario Garafola has known about the investigation for about a year and expects to clear his name at trial, his attorney said.

“We’ve been patiently waiting and looking forward to our day in court,” attorney Scott Leemon said.

Elevator company president Michael Weiss and Frederick Contini, the developer of the headquarters project, pleaded guilty earlier this year in connection with the case, U.S. Attorney Roslynn Mauskopf.

Ms. Mauskopf said in a statement that the defendants carried out a number of schemes at the MTA headquarters, including charging the agency for union labor, using nonunion workers and pocketing the difference.