Bodies of the manatees - four males and a female - were found around the bay between Wednesday and Friday with broken ribs and punctured lungs. They appeared to have been killed by the same large propeller-driven boat, said Antonio Mignucci Giannoni, director of the Caribbean Stranding Network.
"An investigation will be conducted to allow us to clarify what happened there," said Javier Velez Arocho, secretary of the island's natural resources department. He said no suspects have been identified.
Manatees are protected by the U.S. Endangered Species Act, which imposes fines on anyone found guilty of harming animals threatened with extinction.
Puerto Rico has a small population of the large animals, about 300 to 350, Mignucci said.
Four other manatees have been found dead this year on the island's coasts, according to Mignucci. On average, six to nine are found dead each year, many killed by collisions with watercraft.
Manatees are found throughout the Caribbean and are migratory and vegetarian. They live in saltwater but search by instinct for fresh water and underwater plants.