Mr Matahiki was caught between a disused frame for a scanner - which should have been removed - and another part of the mutton chain when caught in the back of the head by the foot-long hook.
It forced its way through his skull, coming out beneath his eye, before pulling him further along the chain.
Mr Matahiki had no recollection of the accident but was told by a firefighter friend who got him down that he had hung on the hook for an hour.
Colleagues had supported his body as he hung there, waiting for the hook to be disconnected.
It was again highlighted in court today that Mr Matahiki was in an area he wasn't meant to be - he was standing on a tray which was out of bounds to staff, but likely used it to check the quality of cleaning on the moving hooks.
However, Judge Rollo refused to count this as a mitigating factor against the company's sentence, telling its lawyer, Mark Hammond, that it had failed to follow its own safety regulations and that the accident should not have been allowed to have happened.
"Ultimately, if the protocol of the company had been promulgated ... we wouldn't have this problem."
Judge Rollo noted how, before the incident, Mr Matahiki had been an easy, outgoing and confident man, but now suffered nightmares and interrupted sleep, was reluctant to leave his home and had already been admitted to hospital with mental health issues that were unlikely to cease.
The emotional and psychological effects on Mr Matahiki, he said, had been "profound".
As Mr Matahiki earlier told the Herald: "My recovery ended up with me trying to commit suicide."
Judge Rollo also discounted Mr Hammond's assertion that the event was a freak occurrence and an "extraordinarily unfortunate accident", and again pointed to failures in the company's own protocols.
But he credited Affco for its follow-up actions, co-operation with WorkSafe NZ and its "positive support" of Mr Matahiki, who this month had been able to return to work in a five-day-a-week, six-hour-a-day role.
However, the estimated loss of income to Mr Matahiki following the event was put at about $11,000.
The $30,000 fine he ordered Affco pay was at the "higher end" of the lower range of fines that could be handed down under the Health and Safety in Employment Act, which carried a maximum penalty of $500,000.
Closing his summing up, Judge Rollo told Mr Matahiki that the case had been a "long process for you".
"I hope you make full recovery with your physical and mental health, that you get back fully into your workplace and enjoy it again, and that your life is highly successful amongst your family and friends."
Outside court, Mr Matahiki and his visibly frustrated supporters declined to comment on the sentence but New Zealand Meat Workers Union organiser Darien Fenton, who attended the hearing with the group, expressed her dissatisfaction.
"I think the fine is pretty much on the light side given the enormity of the injury to Jason," she told the Herald.
"I'm pleased he's been given some reparation, so I think it'll help his family, but I think there is disappointment about the fine."
Ms Fenton said the matter had been a "horrific story".
"It's a horrific injury - that worker has been to hell and back ... [the sentence] sends a message, but I would have liked to have seen a stronger message than we got today with that fine."
But she still believed the court process had been worthwhile.
"In the end, all WorkSafe can do is put it before a judge and the judge makes the decision - in the end, I think WorkSafe has done a very good job in pursuing this case."
In a statement this afternoon, WorkSafe NZ chief inspector Keith Stewart said there were a number of steps Affco could have taken to keep Mr Matahiki safe while he was at work.
"They could have ensured there was a robust lockout process in place and that staff training regarding lockout processes, was up to date and current," Mr Stewart said.
"The company should also have ensured lockout processes were strictly adhered to, that the mutton foreleg chain was not operational as part of the cleaning or inspection process, and that all potential trapping points were identified and managed.
"While this accident reinforces the need for organisations to be continually vigilant in the management of risk, sadly a man now has life-changing injuries that leave him in constant pain."
