The freak incident happened at Downings Pier earlier this afternoon.
The man was named locally as Patrick McGeever from Carrigart who is in his 40s.
Mr McGeever was unloading a crabbing boat when the incident occurred during high winds just before 1pm.
It is understood the truck door which the injured man was loading blew of its hinges and struck Mr McGeever.
It threw him more than 40 feet down onto the deck of the boat which was being unloaded leaving him unconscious.
The emergency services were called immediately and the injured man regained consciousness.
It is believed Mr McGeever has suffered leg, chest and head injuries.
One eye-witness said it was just a freak accident.
“The winds are very strong and very gusty. It was quiet one minute and then all of a sudden they just whipped up.
“I didn’t see it exactly but it appears he was just thrown onto the deck of the boat. It’s a fair drop and I think he’s in a bad way.
“The ambulance was here very quickly and nobody wanted to move him,” he said.
A spokesman for Malin Head Coast Guard Radio station confirmed they alerted the Mulroy Coast Guard and ambulance service who were on the scene in minutes.
However the Rescue 118 Helicopter from Sligo was then scrambled to the scene.
Mr McGeever was taken manually form the boat to the local GAA pitch where he was then transferred by helicopter to Letterkenny General Hospital.
His condition is described as stable.