Michael Schmidt says members of the Canadian Food Inspection Agency seized computers and boxes of items from the farm northeast of Durham on Thursday.
Schmidt, who recently won the right to appeal his conviction for producing, selling and distributing raw milk, says he may face new charges but he's not worried.
Canadian Food Inspection Agency officials would only confirm that they executed search warrants Thursday as part of an investigation into the removal of 31 sheep from an eastern Ontario farm on April 2.
Those sheep had been quarantined over concerns they had a disease known as scrapie and their removal breached a federal quarantine.
Schmidt says he has nothing to do with the sheep's removal, but he has voiced concern in the past about sheep being seized and euthanized by the agency, when he says they may not have been sick.
The dairy farmer was placed under probation in November 2011 for a year and fined $9,150 for operating an illegal cow-share business.
The conviction came after a lower court had acquitted Schmidt of all charges in January 2010. He was granted leave to appeal the conviction late last month.
In Canada, it is illegal to market, sell, distribute unpasteurized milk or cream.
Health Canada warns that raw milk contains several harmful bacteria including salmonella, E. coli and Listeria and can cause vomiting, diarrhea, kidney failure, miscarriage and even death.
But supporters say unpasteurized milk has many health benefits and argue they have the right to decide what they can consume. All milk sold commercially in Canada has been pasteurized since 1991.