Otago's increased 0.7% compared with 2015 to 3.94million head and Southland's increased 2.5% compared with 2015 to 4.3million head. Otago and Southland represented 16% and 14% of the national sheep flock respectively.
In Otago, lambs were marginally heavy compared with the corresponding period last year, albeit only marginally according to farmers.
Some farmers commented on the need for more sunshine to improve lamb thrift, and excessive pasture cover leading to a decline in pasture quality.
A "real balancing act" was in play for farmers over the timing of new season lamb drafts, the report said.
That was between a steadily declining schedule price, which would normally encourage lambs to be processed early, and an abundant feed supply which might encourage farmers to hold stock for longer so as to put on more weight.
An increase in the number of lambs processed early occurred in Otago last year due to the threat of a forecast El Nino weather pattern which often led to a dry summer.
The seasonal outlook for this summer was for more neutral conditions and the need for farmers to send lambs away for processing was not as urgent as previous years.
Beef and Lamb New Zealand Economic Service chief economist Andrew Burtt said that there had been a 1.3% drop nationally, or 0.3million fewer lambs, than last year.
There would be 19.4million lambs available for export in the 2016-17 season, down an estimated 2.7%.
Lamb export receipts for 2016-17 were estimated at $2.5billion, slightly down on the previous season.