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Farmers should prepare for a "very long" processing season, Silver Fern Farms chief executive Simon Limmer says.
While the company had managed to keep Omicron out of its plants, the outbreak had put pressure on its processing chains.
There had been high rates of absenteeism across its network as staff had to self-isolate.
Much as with the overall outbreak in New Zealand, Silver Fern Farms had experienced a "north to south" wave.
It first started to impact its North Island plants about a month ago, and its South Island plants followed afterwards.
While it had meant reduced capacity, the outbreak had been short-lived and Mr Limmer hoped the worst was now behind them.
"It has had a productivity impact, but we’ve managed to step our way through the challenges," he said.
The drought in Southland and parts of Otago was also adding to the pressure on its chains.
Silver Fern Farms’ livestock team was working with farmers to understand the situation and what contingency plans were available.
The company was prioritising based on animal and farmer welfare to ensure those that needed processing space got it first.
"It is really unusual circumstances in the lower South Island, and unfortunately it’s overlapping with Omicron," he said.
Mr Limmer said within the next week productivity would be returning closer to normal.
The current season had already started late due to impacts left over from last year, such as the shortfall in labour.
Farmers, right across the sector, had to be prepared for a "very long" season.
"We are talking to our farmers weekly ... to ensure there is a degree of comfort as we work our way through it," Mr Limmer said.