Over 100,000 lambs are thought to have died in the spring storm which hit central and eastern parts of the North Island earlier this month.
Heavy rainfall and strong south-easterly gales blasted Wairarapa and Hawke's Bay unrelentingly in the first week of September.
A senior analyst at AgriHQ, Mel Croad, said the conditions had made for a tough environment for new born lambs.
"It couldn't have come at a worse time for sheep farmers, with many right in the swing of lambing. Individual farmers are counting losses in the hundreds, and some the thousands," Ms Croad said.
Some farmers had reported their losses may account for 20 percent of their lamb crop, a devastating blow to farm incomes and farmer morale, she said.
"Total lambing losses across the island are expected to be over 100,000 head. This is going to result in a significant dent in the 2018 lamb crop tally, in a season when the lamb crop was already estimated by industry to be the lowest on record," Ms Croad said.
Ms Croad said about 23 million lambs were born last spring, but she did not expect that to be matched this year.
But Beef and Lamb chief economist Andrew Burtt said while the losses were very difficult for the farmers affected, he did not think it would have much of an impact to the lamb tally on a national scale.
"There might be a few hundred thousand ewes having their lambs that week affected by it [the weather] but out of 27 million sheep in total and 17-18 million ewes it's not that significant... on the other hand, if it's on your property it could severely impact your income," Mr Burtt said.
"If you're there and you've suffered, I don't know, 30-40 percent losses of your lambs then it's devastating for you individually," he said.