The region which had the sharpest fall was Canterbury, with 255,000 fewer sheep than the year before.
Manawatu-Wanganui and Otago were the most significant sheep farming regions in the country, each boasting 5.3 million sheep.
Meanwhile, dairy cattle numbers rose by 3 per cent.
This was mainly due to increases of stock in the South Island, said Stats NZ.
Southland in particular saw a boom in dairy cattle numbers, with an increase of 14 per cent compared with 2013 figures.
However despite fluctuations, the number of dairy cattle was still easily outstripped by sheep in New Zealand.
With just under 7 million dairy cattle counted at the end of June last year, there were more than four times as many sheep in the country.
According to Stats NZ figures for the human population at the end of June last year, there would have been enough sheep for every New Zealander to have six of their own.