Animal activists raided the Gippy Goat Farm and Cafe in Gordon Rd, Yarragon on Saturday morning.
About 40 to 50 activists entered the farm when the front gates were opened at 6.45am.
Sergeant Dean Waddell of Warragul Police said a goat, a sheep and a kid were stolen from the property and placed in the back of a van and driven away.
He said when he arrived at the farm the activists were threatening to remove the entire herd which consisted of about 1000 goats.
Sgt Waddell said he eventually urged the group to leave the property, which occurred at about 8.30am.
He said investigations into the theft of the animals was continuing.