A 53-year-old man died after a tractor ran over him at a Yarra Valley winery as he was harvesting grapes on the Wandin East property on Thursday.

A second farmer, a man, 47, died in hospital on Thursday after suffering serious injuries in an accident involving a tractor at Myrrhee, about 50 kilometres south of Wangaratta, on Tuesday.

The deaths follow a 68-year-old farmer being struck by a tractor on at his farm at Meredith, near Geelong. The man, who suffered serious head injuries, later died later in hospital.

WorkSafe director Marnie Williams called the three deaths "alarming".

"Each one of these incidents is a tragedy and our thoughts are with the families, friends and colleagues of these men at this difficult time," she said.

"Tractors are an important farm tool but they are involved in more farm fatalities in Victoria than any other piece of equipment. It is critical that safety is at the forefront of everyone's minds when working with or around tractors."

Ms Williams said farmers must be provided with appropriate training and instruction to ensure their safety, especially during busy times such as the current grape harvest.

"This includes all workers, whether they are full-time, part-time or casually employed," she said.

Ms Williams said equipment, such as tractors, needed to be properly maintained.

"Workplaces must review their safety processes and ensure all hazards are identified and either removed or controlled," she said.

WorkSafe is investigating each of the deaths.