Federal authorities filed drug trafficking charges Friday against three men allegedly involved in a deadly shootout with US Customs and Border Protection agents off the coast of Puerto Rico.

One agent was killed and two more were injured after men travelling on a boat headed toward Cabo Rojo on a key smuggling route exchanged fire with a routine patrol, according to an FBI statement Friday.

The agency is leading the investigation into the shooting.

One of the men on the boat was shot, while officers arrested three more, two of whom were detained on a nearby boat, the release said.

The three men, identified as Edgardo Luis Matos Santos, Osvaldo Hernández Camacho and Nelson Rivera Suárez, were charged with conspiracy to possess with intent to distribute more than five kilogrammes of cocaine while on board a covered vessel.

The two agents injured are being treated in a nearby hospital.

As of Thursday, CBP reported they were in stable condition.

The FBI said it would continue to investigate the incident and the United States Attorney's Office would prosecute the case.

“This is a tragic event,” said W. Stephen Muldrow, US attorney for the District of Puerto Rico in a statement.

“We are going to ensure that those responsible are held accountable.”

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