The crash was reported shortly after 2 pm local time (0600 GMT) and emergency responders were seen lifting a body out of the water.
"Fire services found an unconscious man in the vicinity, and he died at 3:55 pm," a government spokesman told AFP.
A spokesman for the Civil Aviation Department said in a statement that the man who died was the pilot, and the plane was a single engine Zlin Z42.
He said the plane fell into the sea near Hong Kong's rural Tai Po region, located in the city's outlying New Territories.
"There was a pilot and no passengers when this incident occurred," the spokesman said, citing information provided by the Hong Kong Aviation Club.
Police said a person fishing nearby was among those who reported the incident, while a police spokeswoman told AFP that some of the wreckage had been located.
Footage from Cable Television news showed helicopters and police boats assisting in the search and rescue operation.
"The plane had fallen into the water vertically and there was no explosion, there was a bit of oil in the water," an eyewitness identified as Mr. Kwok told Cable News.
Footage also showed firemen fishing the body out of the water.
In October of 2013, a student pilot and an instructor survived a helicopter crash in the city's Shek Kong Airfield.
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