While it had meant reduced capacity, the outbreak had been short-lived and 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.
Listen to Jamie Mackay interview Simon Limmer on The Country below:
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.
Limmer said that 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," Limmer said.
