Emergency services were called on Wednesday morning to the Lockhart River region, in Cape York, after reports the plane was missing at about 11.30am.
The wreckage of the plane was found at about 1.20pm on a beach east of the Lockhart River Airstrip.
The charter flight was believed to be carrying government workers, The Courier Mail has reported.
It is unknown if there are any survivors.
The aircraft, believed to be a Cessna 404, was last heard from at around 9.30am when it made two attempts to land.
High winds and heavy rains have been battering the area due to a tropical low that is expected to develop into a cyclone over the Coral Sea at the weekend.
More to come.