Plant manager Sean O'Neill said the clause only related to "kill days", not short processing weeks.
"But it does not make commercial sense to call out staff to work for say two hours and have to pay the four-hour minimum when supervisors already at work doing other things can carry out the work," he said.
In his determination, Michael Loftus said a commercial decision could not be made if it contravened "an express contractual provision".
Because a rework rate was in the collective agreement, it "actually confirms it is work covered by the collective".
"Finally, I agree with the submission that, while business common sense may assist with contractual interpretation, it cannot be used to override a clear provision."
Silver Fern Farms communications manager Justin Courtney said the matter was only pertaining to the Whakatu plant. "We are reviewing our practices and implications," he said.
Silver Fern Farms has three Hawke's Bay plants: Wairoa, Whakatu, and Takapau, which employs 1000 people at the height of the season.