Beef and Lamb New Zealand's annual stock number survey showed a 2.6% increase in sheep and a 1% increase in the beef herd.
That partly made up for the 4.4% decline in sheep and 2.6% decline in beef cattle the previous year, Beef and Lamb economic service executive director Rob Davison said.
Most of the increase in sheep numbers would be stock carried over for slaughter in July-September, Mr Davison said.
Otago had one of the largest increases in sheep numbers, up 4.5%, reflecting better feed conditions than previous years and more trading stock.
Hogget numbers in the region increased 11.7% on the previous year, and beef cattle numbers decreased 5.6%, or 13,000 head.
Nationally, breeding ewe numbers at 20.61 million were almost static (up 0.6%) on the previous June when ewe numbers fell 6% to a low of 20.49 million.
The only region to record a drop in sheep numbers was Marlborough-Canterbury, which decreased slightly (down 0.8%) on the previous year from land-use change, particularly to dairy.
Strong mutton prices earlier in the year encouraged a high slaughter of cull ewes for the second consecutive year. The offset to that was a high retention of ewe hoggets (up 10%) last July.
Federated Farmers meat and fibre chairwoman Jeanette Maxwell said the survey showed what a couple of good back-to-back seasons could do for stock numbers and morale.
But while lambing numbers and calving prospects were looking good this season, key export markets were struggling and every stock unit would be needed to bridge an income gap because of falling prices, she said.
A projected increase in the lamb crop could help offset reduced farm incomes. What was "not looking flash" was the "tanking wool market", Mrs Maxwell said.
Scanning results led to expectations the 2012 lamb crop could be up 4% on last spring, or one million lambs. An excellent spring was now needed to ensure high survival of the lambs born, Mr Davison said.
Beef cattle numbers in the South Island were down 5.7%, which was attributed to an earlier slaughter because of good seasonal conditions so fewer cattle were on hand at June 30, coupled with pressure from alternative land uses, including dairy grazing.
North Island beef numbers increased 3.6% with increases in both the beef cow herd and weaner cattle numbers.
The economic service estimated the dairy herd increased 3.2% with part of that increase a carry-over of older cows in the North Island because of excellent growing conditions.