Some farmers have been forced to bait repeatedly in a bid to protect their crops, while crops in some paddocks have been abandoned and given over to livestock for grazing.

Some blooming canola crops near Horsham and throughout South Australia now resemble blocks of Swiss cheese because hungry mice either ate the seeds at sowing time, or have snipped off the top of the plants.

Rupanyup farmer Andrew Weidemann said the main crop affected in his region was canola, where "plants are being chewed off at the head".

“Now, because the temperatures are starting to increase, the concern is that we're going to see more of it, and of course the baiting is still continuing," he said.

“We're really not getting on top of the problem. There's an underlying amount of mice that are just continuing (to survive). The baiting is not effectively getting rid of them, it's just keeping them at a low level and then they explode with the right weather conditions and then you have problems.

“In some paddocks we've seen 60 and 70 per cent damage in the Wimmera, and more so in the Mallee.” 

Steve Henry, research officer with the CSIRO, is examining the prevalence of mice in cropping systems across Australia with funding from the Grains Research and Development Corporation, to try and provide a warning ahead of mouse outbreaks.

Mr Henry said recent field work in Victoria indicated a higher level of mouse activity in early spring than seen in the previous five years.

"At the moment we are quite concerned about the Victorian Mallee and the Wimmera, because I've trapped higher numbers than I would normally expect to trap in the spring," he said.

"That means if they're presented then with favourable conditions, in that there's food and shelter and climatic conditions are favourable, then we would expect them to continue breeding through the summer and into the next autumn and there could be potential damage in the next autumn when we're sowing the 2018 crop.

"I know of farmers who've spent up to $100,000 on mouse baits since they started sowing the crop this season. There's been a huge amount of money spent," he said.

Asked if Victoria was experiencing a mouse plague, he said: "It's not a plague at the moment."

Victorian Farmers Federation president David Jochinke said Wimmera farmers faced "absolutely horrendous" mouse numbers when they sowed crops in April and May.

"We had an excellent harvest the previous year, which meant that as the crops matured they spilled grain onto the ground, and (we had) ideal breeding conditions – warm, a lot of feed, a lot of ground cover so they could hide from their predators. So they bred up into some extreme numbers," he said.

"We spent roughly $32,000 trying to manage mice this year ... but not only did we have the cost of baiting, we had the cost of sowing the paddocks twice, as well as the yield penalty of sowing it late.”