It's believed grain pellets were being unloaded from the truck into the loader's bucket in the late morning when the loader moved forward, trapping the worker.
Ambulance Victoria attended the scene and the man was treated but he died from his injuries.
WorkSafe Victoria and the Victoria Police Major Collision Investigation Unit attended the scene.
Last week a man died during a harvesting machine incident on a Gembrook farm, east of Melbourne, while working alone.
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In May, a man had also died while working on a farming property in Crowlands, about 20km northeast of Ararat.
The incident in Cowwarr is the seventh workplace death that has occured in the agriculture, forestry and fishing industry this year.
The workplace fatality toll for 2022 now stands at 28, which is six fewer than at the same time last year.
Worksafe Victoria are investigating the incident and a report will be prepared for the Coroner.
