Police say they were alerted to the discovery at about 6am yesterday by a local fishing charter operator preparing to head out to sea for the day.
The body of the middle-aged man was seen in the water near the wharf where the charter boats moor.
Police teams, including scuba divers, were at the scene yesterday morning.
Another police team went to Rarotonga Hospital where they talked to medical staff about the body.
Police refused to release many details of their investigations yesterday.
However, they did say the man was aged 59 years old, was a Rarotonga resident and had a work permit for a local company.
A medical report from local authorities was expected late yesterday.
Meanwhile, a pathologist has arrived from New Zealand to conduct a post mortem today on the elderly woman whose body was found last Thursday at Kavera Beach.
The woman, believed to be in her 70s, was discovered on the beach after 7am. It was found by a tourist out for an early morning walk.
The post mortem will take place at the morgue and police will be in attendance while the medical investigation is carried out.
It is understood the pathologist may give an early, verbal indication of their findings into the cause of the woman’s death.
However, the formality is that the pathologist has to go back to New Zealand and finish their report from there.