Paramedics and a rescue helicopter were dispatched following the crash just after 8am on Friday at Ball Bay, about 50km north of Mackay.
Police confirmed the Kuttabul man, a passenger on the plane, died at the scene.
The 65-year-old pilot, of Haliday Bay, was airlifted to hospital with minor injuries.
Australian Transport Safety Bureau chief commissioner Angus Mitchell said the amateur-built Jodel D11 light aircraft was recovered ahead of a rising tide and would be examined by investigators.
"The ATSB will analyse any recorded data, as well as interview witnesses and other involved parties," Mr Mitchell said.
"A final report will be published at the conclusion of the investigation, however, should any critical safety issues be identified at any stage during the course of the investigation, the ATSB will immediately notify relevant parties so appropriate safety action can be taken."
Anyone who saw the aircraft, has footage or knowledge of the operation of the plane is asked to contact the ATSB.
The incident follows the death of four people in a light plane crash north of Brisbane less than a week ago.
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