The conditions affecting the goats included a combination of cancer of the eye, severe lameness, severely distended udders, infected udders and foot disease.
Ministry of Primary Industries prosecutor Morgan Dunn said transporting the goats in this condition had caused the animals unreasonable and unnecessary pain and distress.
Mr Dunn submitted a fine of $10,000 was the appropriate starting point before allowing a discount for the defendant's guilty plea and mitigating factors.
The defendant's lawyer argued the ministry's starting point of $10,000 should be halved, given there were "considerable mitigating factors".
That included that his client had engaged a farm manager who was responsible for the daily operations who may have over-represented their skills and experience, he said.
The defendant had an "otherwise unblemished" animal welfare record supported by character references, including one from a veterinarian, and the directors reassured the court they would take steps to ensure this never happened again, he said.
Judge Paul Mabey QC said it would have been "inescapable' to anyone that these animals should never have been transported to the meatworks in this condition.
Under the Animal Welfare Act, the defendant was ultimately responsible, he said.
But Judge Mabey said given the defendant's lack of prior convictions, and the other mitigating factors, he was satisfied a fine of $4500 was the appropriate sanction.