Witnesses said the crash happened shortly after the plane took off.
The pilot, a middle-aged man, managed to get out of the plane on his own, observers said.
In its overnight report, the Royal Newfoundland Constabulary said the pilot had been brought to shore by boaters in the area.
There was no one else in the aircraft.
He was picked up from the island by the St. John’s Regional Fire Department’s coldwater rescue team in a small watercraft.
The man was assessed by Eastern Health paramedics and taken to hospital by ambulance. His injuries are not believed to be life threatening.
The Investigation has been turned over to the Transportation Safety Board of Canada.