The man died when he was rushed to hospital after being pulled unconscious from the water by a rescue boat.
Hong Kong's harbour race is under review along with future open water events globally after the death of a swimmer at the weekend, the world aquatics governing body said.
The man died when he was rushed to hospital after being pulled unconscious from the water by a rescue boat Sunday during the city's annual event, which attracts world-class international competitors and recreational swimmers.
"FINA is very sad to hear of the unfortunate incident," the governing body said in a statement Monday.
"We will be conducting a thorough review of the incident and the overall safety and organisation of future outdoor mass participation events," FINA said, adding it was working closely with race organiser the Hong Kong Amateur Swimming Association and other groups responsible for similar events around the world.
The 1,500-metre (4,900 feet) race saw around 3,000 people swim between two piers on opposite sides of Hong Kong's famous harbour -- 500 up from the previous year according to reports.
Some local media questioned why only 10 extra lifeguards had been added when the field had expanded so much. There were 120 lifeguards at the event, broadcaster RTHK reported.
A 59-year-old woman was also pulled out of the water unconscious and is in hospital in intensive care, a race spokesman told AFP Tuesday.
Both harbour race victims were taking part in the leisure category, which is for slower swimmers.
The Hong Kong Amateur Swimming Association and the title sponsor New World Development have expressed their "deepest sorrow" over what they called a tragic accident.
It is the first death in the race since it resumed in 2011 after a 30-year break, local media reported.
The decades-long hiatus was because of fears over pollution levels in the water.
Hong Kong is one of the world's busiest ports, with more than 400,000 vessels arriving and departing annually.