Stats NZ's new Agricultural Production Census for 2022 reveals the national flock dropped two percent on the year before, to 25.3 million sheep in June 2022.
The five-yearly survey of farming production and practices came under fire by farmer lobby group Groundswell.
It urged those in the industry not to fill out the survey, because it disagreed with the tools Stats NZ used to measure agricultural emissions.
But Stats NZ's general manager of economic and environment insights Jason Attewell said more than 42,000 farmers, growers and foresters took part, at a response rate of about 73 percent.
He said that was "slightly" down from 85 percent in the 2017 survey.
"We were aware of the Groundswell campaigns for farmers and other people not to fill out the Agricultural Census," Attewell said.
"What we found was when people refuse to fill out the survey, and said that was the reason, it was less than 0.5 percent of the response rate. The response rate was not as high as we would like it to be, at 73 percent, but we're still really confident in the data.
"Agriculture is so important to our New Zealand economy, so it's a really important industry to know about," he said.
The latest figures also saw the national dairy herd dropping off historic highs - from 6.7 million cows in 2014, down 8 percent to 6.1 million in June.
Beef cattle numbers have stabilised at 3.9 million.
Land planted for kiwifruit continues to grow for the gold variety - soaring 154 percent to 7800 hectares over the last decade, while acreage in green kiwifruit dropped by a third.
Kiwifruit was still the country's largest horticultural export by value, and covered a total planted area of 14,700 hectares in 2022.
By Monique Steele
