Lamb numbers in Otago dropped by 68,000 this year, as poor weather over the peak of lambing on the hill country and a decrease in the number of ewes mated contributed to the decline.
Beef and Lamb New Zealand has released its annual lamb crop survey, which showed total lambs in the region were down 1.6% to 4.2 million head.
In Southland, total lambs decreased 6.9% to 4.41 million head, a drop of 326,000.
That was driven by a continued decline in the ewe flock, fewer hoggets mated and a small decrease in the lambing percentage.
In Otago-Southland, overall lambing was variable.
Reports ranged from ''best ever'' to ''very disappointing'', the report said.
The ewe lambing percentage decreased 0.9 percentage points to 121.7% in Otago and 137.1% in Southland.
While weather conditions were excellent during late August and September, cold wintry periods in October coincided with lambing on hill country and hogget lambing on the lower country.
Salmonella brandenburg, which had an impact across Southland and parts of Otago, caused significant decreases in lambing percentage on some affected farms.
Drought two years ago continued to have an impact and there was only a modest improvement in numbers tailed nationally this spring, Beef and Lamb New Zealand economic service chief economist Andrew Burtt said.
An estimated 25.8 million lambs were tailed, up 1.2% on the previous spring. However, last spring was the second smallest lamb crop in nearly 60 years.
This season's crop was still feeling the impact of the drought that affected most of the North Island and parts of the South Island in 2012-13, Mr Burtt said.
Numbers were up 5.5% in the North Island, while 2.6% less lambs were tailed in the South Island.
With overall lambing performance in the South Island virtually identical to 2013, the figure of 13.4 million head was a direct result of fewer breeding ewes, due to land use changes to dairy and dairy support activities, particularly in Southland.
Fewer lambs were expected to be processed during 2014-15 compared with the previous season. The number of lambs available was estimated at 19.95 million head, compared with 20.3 million last season.
However, the background reasons were positive, as farmers were holding on to lambs so they could rebuild sheep numbers, particularly in the North Island, Mr Burtt said.
The market outlook for lamb appeared to be stable at this point, the report said.