Leonardo Perez Meson was arrested after his boat ran aground on the seashore in the southern town of Patillas, the police said in a statement.
An anonymous telephone call alerted the police, which also seized a vehicle that was found at the site, although several other people who were with Perez Meson managed to escape.
Puerto Rico Police Department (PRPD) and Federal Bureau of Investigation (FBI) agents are continuing the investigation at the site of the arrest.
The main cause of criminality in Puerto Rico is the violent jockeying among criminals for control of drug sales points on the streets of the island.
Puerto Rico is used by drug trafficking networks as a conduit for introducing illegal drugs into the continental US.