This year 12 train services have struck and killed 70 sheep and one dog.

V/Line has warned the cost to commuters through delays and repairs is becoming unacceptable.

In one of the more serious cases a VLocity train near Beaufort was forced to stop after ploughing into a flock of 400 sheep on April 24.

Last month flocks of more than 100 were also reported on tracks near Beaufort twice in the same day. V/Line spokesman Daniel Moloney said near-misses also occurred regularly at Deer Park and Ballan involving sheep, goats

and horses.

The average delay to a service after stock have been killed has been about 10 minutes, but last week 17 cows struck by a train on the Warrnambool line caused at least $10,000 damage and a delay of several hours.

"(Sheep) usually just cause delays to a service and some minor repairs when they get to Ballarat or Melbourne station, but it's obviously a costly exercise for farmers who have sheep or other animals on the rail reserve," he said.

"We are appealing for farmers to tend to their fences, because we are seeing a spike, particularly on the Ballarat line, with animals on the tracks.

"One of the difficulties is trying to even identify a landowner. We can't get access to their details to let them know their fences are in bad shape."

Mr Moloney said V/Line was working on a pilot program with councils along the Warrnambool line to allow council officers access to train lines to impound livestock.

"At the moment we are looking to help out councils a bit more and seek impoundment of the animals."