Livestock already loaded onto trucks are being turned back in Hawke's Bay because workers are choosing to pick fruit over labouring in the meatworks.
Craig Hickson, of Progressive Meats in Hastings, said his company was facing "unprecedented absences" from its processing line.
"This year has been without precedent with regard to the availability of staff for our enterprise."
It wasn't just his industry struggling, the issue had been exacerbated by Covid-19-related travel restrictions for overseas workers, he said.
"It's a reduced supply of labour.
"It's not just impacting on ourselves but also why we have a high demand for horticulture and viticulture industries."
Staff shortages at the meatworks were an "indirect effect" of this, he said.
Having operated at their Hastings site for more than 40 years, he said it had never been an issue for them in the past as they operated year round.
"Labour is always a challenge in our industry but here at our plant in Hastings we had quite a good source of labour.
"We never really felt the competition with seasonal requirements.
"We are being impacted in an unprecedented way."
He said legislative changes around minimum wage and sick leave allowances had also contributed to the problem, with "increased claim rates for sick pay".
The staff shortage had struck at a particularly difficult time for the plant which primarily processes lambs.
"Last year when Covid-19 hit, we were largely through the season.
"It's occurred during the peak of the season."
He said they were currently recruiting, a big point of difference being that they work year round, providing steady income opportunities.
"We have jobs available."
Federated Farmers Hawke's Bay president Jim Galloway said it was an issue facing many processing plants around the region.
"I've heard of one farmer who had stock booked in [at an unnamed processing plant] October. He might have had 500 booked in but they only took about 200.
"They are not taking them or people are getting their numbers cut back."
He said it was "frustrating" for farmers and difficulties getting stock off farm was definitely a concern.
Alternative employment and competition for labour had also been a problem but he acknowledged wages in the horticulture sector had "come up quite considerably" in recent months.
"It's making it harder.
"We always need new people. It's a shame because there's so many opportunities."
While things weren't as dire as during last year's drought, it was still difficult timing as there wasn't a lot of quality feed available for younger stock and lambs with concern about stock weights dropping.
"Lamb is the critical one to get off [at the moment]. The peak season is now."
Galloway said farmers needed to starting planning early, particularly as Thursday's thunderstorms were expected to be quite localised.
"We are always thinking one or two seasons ahead.
"If there's a delay you need to be in the queue."
Mr Yummy apple grower and owner Paul Paynter said the industry was still facing a labour shortage of its own, with Hawke's Bay in need of thousands more for the harvest season.
He said it was difficult to know if people were leaving meat processing plants for apple picking but felt this was unlikely.
"I would expect that they are much more attractive as an employer.
"I think people are more likely to work there than to spend all day climbing up and down ladders in the hot sun picking."
Paynter acknowledged orchard owners were paying higher wages, but said this still wouldn't be enough and it was going to be a "difficult season".
"We are desperate for pickers.
"We are not going to get all the crop in.
"I'm concerned about how the numbers stack up."
He expected the reduced harvest to negatively impact the Hawke's Bay economy - Paynter said the apple industry was worth about $500 million to the local economy.
"We are going to be quite badly affected."