Kevin McLeod's body was found in Wick harbour in February 1997.
His family believe he was murdered and complained to Northern Constabulary about its handling of the case.
The Police Complaints Commissioner for Scotland (PCCS) said it will investigate how the force responded to that complaint.
Their complaint centres on the claim that the procurator fiscal instructed the force to carry out a murder investigation.
Northern Constabulary has treated Mr McLeod's death as accidental, but his family have consistently criticised the force over its investigation.
In 2007, the PCCS said Northern Constabulary behaved with "institutional arrogance" in the way it handled earlier complaints from Mr McLeod's parents, Hugh and June McLeod.
It ordered the then chief constable, Ian Latimer, to apologise in person to his relatives. The senior officer went on to do so.
Northern Constabulary said it could not comment on the latest PCCS investigation.
A spokeswoman said: "Northern Constabulary has investigated all known evidence thoroughly and extensively.
"The case has also been subject to fatal accident inquiry and internal and external reviews, over a number of years since 1997.
"Northern Constabulary remains willing to examine any new information, should this come to light, but there is currently no evidence to suggest any criminality."
A police force's handling of a complaint from the family of a man who died 16 years ago is to be investigated.