NEW YORK — The Secret Service has broken up one of the biggest U.S. manufacturing operations of bootleg CDs ever uncovered.

The Treasury Department agency, best known for nabbing counterfeiters and protecting the president, shut down a factory here that had the capacity to produce 3 million high-quality pirate CDs a year, complete with counterfeit labels and shrink-wrapped CD “jewel box” cases.

The Recording Industry Association of America (RIAA) estimates that the bootleg CDs would have cost record labels $47 million in annual sales.

The crackdown began when Secret Service agents descended on a garage in Queens on March 8 that was rigged up as a pirate’s paradise. The agents found 90 CD burners, 16 cases of counterfeit CDs, a shrink-wrap machine, blank CDs and CD jewel boxes.

In a later raid in Manhattan, agents recovered more than 17,000 counterfeit CDs ready for sale on the street. In record stores, the real CDs sell for about $15 or more each.

A partial list of the CDs shows that the bootleggers’ taste ran toward urban and Latino music, with a sprinkling of pop. Included: Tito Puente, Jay-Z, Julio Iglesias, Santana, Jennifer Lopez and The Beatles.

The RIAA described the business as a “massive counterfeit music operation.”

Says Bruce Townsend, who heads the Secret Service’s financial crimes division: “Any time you’re talking about a $50 million loss to an industry, that’s significant.”

Two men, Richard Certuche and Patrice Benon, have been arrested so far. Although Townsend said he could not comment, it is believed that the investigation is continuing to identify other associates involved in the operation.

The case grew out of a tip from the RIAA to the New York Electronic Crimes Task Force, a 200-member group that consists of several levels of law enforcement as well as private industry groups and representatives of academia.

Because of its expertise in comparable counterfeit activity, the Secret Service coordinated the task force’s efforts to shut down the music production facility.

“(The operation) is an interesting blend of the Secret Service’s historic expertise in forged documents merged with our current expertise in computer technology,” Townsend says.

“The Secret Service regularly investigates high-technology and computer crimes. It’s now part of our investigative mission.

“When new agents finish training, they get a gun, a badge and a laptop computer.”