(CNN) -- Federal agents arrested dozens of airline workers and baggage handlers at Puerto Rico's busiest airport, targeting what authorities say are two drug smuggling rings working together to move cocaine into the United States aboard commercial aircraft.
The arrests at San Juan's Luis Munoz Marin International Airport targeted two drug rings in Puerto Rico, including one that operated through the airport for more than a decade, according to two federal indictments unsealed Wednesday, hours after the raid.
It was the second time in three years that federal authorities targeted drug smuggling at the airport, cases that stem from the September 2009 arrest of American Airlines employees accused of smuggling drugs for one of the groups, according to one of the indictments.
Forty-five people, including 12 current and former employees of American Airlines in Puerto Rico and on the U.S. mainland, were indicted, the U.S. Drug Enforcement Agency said. At least 36 people had been arrested by late Wednesday, including 10 who were picked up in the raid at the airport, the DEA said.
Packages of cocaine and heroin destined for New York, New Jersey, Florida, Pennsylvania, Maryland and Massachusetts were intercepted by law enforcement in Puerto Rico or at their destinations, federal indictments say.
American Airlines said it was assisting local, state and federal agencies in the investigation.
"Our support also extends to helping prosecute the individuals responsible to the fullest extent of the law. We have a zero tolerance policy for any employee when it comes to this type of activity," said Ed Martelle, a spokesman for the airline.
The arrests shine a light on the growing drug trade transiting through Puerto Rico, a strategic location between South America and the United States.
In addition to its location is the fact that Puerto Rico is a U.S. commonwealth, so passengers from there don't have to go through customs upon arriving on the mainland, said Laila Rico, a spokeswoman for the Drug Enforcement Administration.
Puerto Rico's government has blamed drug-related violence for pushing the commonwealth's murder rate to more than five times the U.S. national average. Local officials have described the island's borders as an "under-protected front in the nation's war on drugs."
"We have been asking the federal government to help us patrol ... the Puerto Rican coasts, which we are unable to cover entirely by ourselves," Puerto Rico Gov. Luis Fortuno said Wednesday. "We want them to help us protect it in the same way they protect the borders with Mexico and Canada."
The unsealed federal indictments paint a picture of cooperating drug smuggling rings, including one led by a woman, that recruited airport and airline workers between 2010 and 2012 to help clear luggage loaded with drugs, primarily cocaine and heroin, onto airplanes.
One group carried kilos of cocaine in backpacks, on their bodies or in company vehicles into the airport through security, according to authorities.
Once inside the airport, members of that group would meet couriers inside a restroom, and the couriers would take the drugs and board airplanes for the continental United States, according to one of the indictments.
In that scheme, an indictment charged 25 people with 16 counts each of racketeering and drug trafficking, the Justice Department said.
Several of those indicted worked for a baggage and cargo handling company known as Ground Motive Dependable, said Rico, the DEA spokeswoman.
The second indictment unsealed Wednesday charged 20 people with "aiding and abetting each other" to distribute more than 9,000 kilograms of cocaine aboard American Airlines commercial flights, the department said.
Those arrests are directly related to the 2009 arrests of American Airline workers, who authorities say were recruited by drug smuggling ringleader Wilfredo Rodriguez Rosada, according to the federal court filing.
Rodriguez Rosada surrendered to authorities after the arrests in 2009. He was sentenced to federal prison for his role in the ring that dates to 1999, according to court records.
Federal prosecutors allege in the latest round of arrests that the group moved luggage through security and into cargo holds on airplanes bound for Miami, Orlando, Newark and elsewhere.
Authorities did not specify where the drugs connected with Wednesday's operation came from before they entered Puerto Rico, saying they were still investigating.
Last month, the head of the Caribbean region for the Drug Enforcement Administration told the EFE news agency that increased security at the Mexico-U.S. border contributed to making Puerto Rico one of the principal entry points for drug trafficking in the United States.
A record 1,136 people were killed in Puerto Rico in 2011, the commonwealth's government said in February, calling for more federal funding and resources to begin a "Caribbean Border Initiative" to crack down on drug trafficking and violence.
Journalist Dania Alexandrino and CNN's Rafael Romo, Nelson Quinones, Catherine E. Shoichet, Mariano Castillo, Chelsea J. Carter and Melissa Abbey contributed to this report.