WorkSafe New Zealand's lawyer Richard Jenson argued that after cleaner Jason Matahiki was impaled by a meat hook in 2014, Affco should have identified the knock-off area as a potential hazard and attempted to reduce the risk.
He said Affco had taken a "reckless attitude" to its health and safety obligations.
Affco lawyer Mark Hammond argued that all six of the charges should be dismissed as the Crown had failed to prove its case.
He described the injury as "a freakish accident" that no one could have foreseen.
Mr Hammond said Affco had made a concerted effort to assess any other potential hazards after Mr Matahiki's 2014 injury.
Judge Paul Mabey QC said he accepted Mr Hammond's submission in regards to three of the charges as in this case there was no evidence of prior knowledge of the hazard.
He found there was a prima facie case to answer on the other three charges.
The judge adjourned the trial for written submission from the prosecution and defence lawyers, which will be followed by a hearing on July 21, before he delivers his verdict.
The three charges Affco NZ is defending:
Being an employer, knowingly failed to take all practicable steps to ensure Mr Kordt was not exposed to hazards arising out of his work on the mutton chain at its Rangiuru Plant.
Being an employer, failed to take all practicable steps to ensure that Jonas Kordt had such knowledge and experience of the work or was so supervised by an experienced person.
Being an employer, failed to take all practical steps to ensure Mr Kordt was adequately trained in the safe use of all plant and objects that he was or may be required to use.