Good crop yields in 2019/20 and summer rain since harvest have presented a perfect storm for a jump in mouse populations.
Many areas of the Mallee and Wimmera recorded excellent yields of barley and wheat in particular before wind damaged crops.
Birchip cropper Leigh Hogan said the yields were a positive, as was the good early rains.
However some of his paddocks were showing signs of mouse populations that were reaching worrying levels.
He said strong winds during the 2019/20 harvest had left high levels of grain in already heavy stubbles.
It was very much a paddock-to-paddock proposition, he said.
Paddocks that were harvested prior to the winds were not showing signs of mice, but those harvested after were badly infested with mice holes.
"I have baited wheat and barley stubbles at one farm already. The home farm is not too bad at the moment," he said.
Mr Hogan said lentil stubbles going back into barley were also affected.
Some paddocks had green regrowth from the barley left behind from harvest. Mr Hogan said he had bought some lambs to feed off the growth.
He said some paddocks looked "not too bad" but would be baited to prevent damage later on.
CSIRO research officer Steve Henry said the warnings had been around for some time about potential mouse numbers.
He said mice were a real issue in the southern Mallee and Wimmera.
Estimates were of one to 1.5 tonnes of grain on the ground after the wind event and even after 100mm of rain between Christmas and April, much of that grain had not germinated.
"That equates to a huge amount of food available to mice and plenty of cover," he said.
That led to mice continuing to breed through spring and into autumn.
The issue now was to try to push numbers down to low levels through the winter so when breeding started in spring, they started from low population base.
Mr Henry said farmers needed to walk out into paddocks to check numbers.
Given the reports of mice populations the message to farmers already was to bait at sowing when control was best.