It is not known exactly when they began disappearing, as their absence was only noticed recently.
Police said it was "unlikely the theft of hundreds of animals could be completed at once, and is more likely that multiple thefts could be carried out over a period of time".
The cows are reportedly worth at least NZ$750,000 ($0.5m; Â£0.4m) in total.
A friend said the farmer was "absolutely gobsmacked, and deeply embarrassed".
"If you had three-quarters of a million dollars go missing, you wouldn't want to talk about it either," Willy Leferink told the Associated Press.
Locals told AP they had never heard of cattle rustling on such a scale before.
The farm's original 1,300 cows are thought to have last been counted in July.
Sr Sgt Scott Banfield of Ashburton Police urged farmers to check on their stock numbers once a week.
"Farmers should also be keeping an eye out for unexpected signs of herding near their boundary lines too."
New Zealand is home to around 10 million cows, more than twice the human population.
New Zealand police are investigating reports that 500 cows have been stolen from a farm in Canterbury.