He was injured while using a winch to wind log covers onto a stack of logs.
When the winch wire became entangled, described as a "bird's nest'', the victim hopped off the tractor to clear the mess while the winch was still operating and stepped into the wire rope. The cable wrapped around his leg, resulting in him losing his foot.
Surgeons were unable to reattach his severed limb.
Bream Bay's lawyer Sarah Read told Judge Thomas Ingram her client was remorseful and willing to pay reparation.
Ms Read said the victim had undergone an induction training course.
However, her client accepted there were failures in training for this specific hazard and in the company's health and safety documentation processes. The company also accepted the need for closer oversight of its employees working at the Port.
Remedial action had already been taken, she said.
Genera's lawyer Mark Beech said the company also provided training for the victim but accepted it had fallen short in its health and safety obligations.
Genera did not accept it was equally culpable as Bream Bay but offered to pay a greater share of the reparation to ensure the victim was compensated, and had also taken remedial steps, he said.
Judge Ingram said it was clear the hazard was obvious, and there were therefore health and safety failures by both companies.
Both companies should have ensured they had complementary training material, appropriate health and safety processes and procedures and closer monitoring to ensure employees were not put a risk, he said.
Judge Ingram said although some training had taken place, the overview of their respective safety processes had fallen short. "This is what caused the problem and led to the accident. If the two safety regimes had been meshed and the paperwork signed off and correct steps taken, this accident would never have happened,'' he said.
Judge Ingram said the two companies were responsible employers and had made a mistake.
"The essential point is everyone learns from this and it doesn't happen again.''
In setting the levels of fine and reparation, the judge took into account, the remedial steps already taken, prompt guilty pleas, remorse, co-operation with the investigation, offer of amends, and, in the case of Bream Bay, its ability to pay.
Bream Bay was fined $25,000 and ordered to pay $15,000 reparation, while Genera was fined $20,000 and ordered to pay $25,000 reparation.
Outside court Bream Bay's director Neil Porter declined to comment saying it had nothing to do with him personally, while a spokesman for Genera said the company was satisfied with the outcome, and his thoughts were with the victim.
