The body was found nearly a mile (1.5 kilometers) off the coast in front of the Grand Melia resort late Tuesday morning, said Nino Correa, search and rescue director of the Emergency Management Agency. The victim has not yet been identified.
Crews are searching for the remaining passengers, and Police Chief Jose Figueroa Sancha told NotiUno radio station that officials found the fuselage of the UH-72 helicopter just north of the island.
It is unclear what caused the crash. The helicopter was returning from the neighboring island of Vieques when it disappeared late Monday just north of the coastal city of Rio Grande. One pilot had 10 years of experience and the other had at least six years, and neither reported any problems during the flight, said National Guard Gen. Antonio Vicens.
"The communication disappeared," he said.
Two of the passengers are prosecutors with the local justice department and the other four are officials with the National Guard, three of them crew members, said U.S. Coast Guard spokesman Ricardo Castrodad.
The prosecutors, Francisco Mujica de Leon and Mario Torres Marin, worked for the division of organized crimes, said Justice Secretary Guillermo Somoza, adding that he has known both of them for more than seven years. Torres is president of the Association of Prosecutors.
"It is an extremely sad, difficult and painful day," Mujica de Leon said. "They were extremely dedicated prosecutors who went the extra mile."
The others aboard the helicopter were not identified pending notification of their relatives, officials said.
The helicopter was flying at about 400 feet (123 meters) and was fairly new, having been bought in May 2009, Vicens said.
It apparently changed its route, but it is unclear why.
The officials had been in Vieques to help serve 43 arrest warrants after a seven-month investigation into drug dealers on an island popular with tourists. Several housewives were among the suspects, according to justice spokesman Fidel Rodriguez.
The group is suspected of earning more than $2 million a year, he said.
Among the officials involved in the raid were 36 members of the U.S. National Guard, which has been helping Puerto Rican police battle the island's rising crime.
The U.S. Caribbean territory of 4 million people has registered its third-worst year for homicides, with more than 920 people reported killed this year. A record 995 people were killed in 1994.