This was because of an "operational incompatibility" between the two agreements, and because they had more infrastructure on-site.
The minority of workers would operate on the afternoon shift while the parties tried to find a way to remedy the incompatibility between the two agreements.
"As a reasonable employer, Affco has elected for minimal disruption to the majority of the workforce so to retain those engaged employees on the shift they have been working for the past seven weeks ... while allowing us to promptly engage those remaining workers without delaying start-up."
Mr Ogg said it was not a straightforward situation at the Wairoa plant. "The plant is operating normally now and there are a lot of people who have been working there.
"Assimilating people who have not yet come back is not easy."
New Zealand Meat Workers Union national secretary Graham Cooke said the afternoon shift was a "Clayton's offer".
He said some of the workers offered the shift had been working for 20 years. Every year when the season began they resumed working the day shift as part of their employment agreement.
Two weeks ago, the Employment Court found Affco Talley's had unlawfully locked out union members in order to gain individual agreements to their advantage. In doing so they had undermined the union and collective bargaining.
Mr Tucker said the Employment Court ruled that those on the expired collective agreement at layoff from last season were able to choose between two options.
They were able to choose to accept the new company individual employment agreement they were currently on, or go back to the expired collective agreement but as individual agreements.
The NZ Meat Workers Union said that since the court's decision, union members from various plants faced resistance.
The union was seeking unprecedented judicial intervention in the unlawful lockout of Affco Talley's workers.