The horses, which were travelling in a converted shipping container, were discovered dead in Victoria after sailing north following a tournament in Tasmania in January 2018.
The ferry's operator TT-Line was in March 2023 convicted and sentenced for 29 animal welfare breaches and fined $75,000.
It will now pay $4000 after winning a Supreme Court appeal and having the most serious charge, relating to management likely to cause unjustified pain and suffering, set aside.
Supreme Court judges found no causal link between double-stalling and the polo pony deaths. (HANDOUT/AIRNORTH CABLE BEACH POLO)
The original sentencing magistrate said the container, which was carrying 18 horses, was inadequately ventilated and the animals that died were incorrectly doubled-stalled.
The magistrate also said the company did nothing to check whether the horses were individually stalled, as per requirements, when they "squarely" had an obligation.
Supreme Court judges who assessed the appeal ruled evidence did not establish any causal link between double-stalling and the horses' deaths.
In their June 2023 ruling, they said the magistrate erred by holding TT-Line responsible for relying on a declaration by a transport operator that the horses had adequate ventilation.
In a decision delivered on Friday, Justice Alan Blow said TT-Line had as a result "uncontroversially" contended the original fine should not stand.
Justice Blow said there was no suggestion being double-stalled caused or contributed to the horses' deaths.
However, he said the breach of the single-stalling requirement was "so serious" a conviction and fine must still be imposed.
Justice Blow said the single-stalling regulation had existed for more than four years before the 2018 deaths.
A judge said TT-Line has suffered adverse publicity over the horse deaths and court proceedings. (Bianca De Marchi/AAP PHOTOS)
"It is true the company routinely obtained declarations from drivers (about animals being single-stalled) but it is clear double-stalling routinely occurred," he said.
A vet told the court the purpose of single-stalling was to prevent horses from biting, kicking or fighting and there was no suggestion the requirement related to ventilation.
Justice Blow set aside all the charges bar two, which related to double-stalling, and imposed the reduced fine.
He said recording convictions on all 28 charges could create an inaccurate impression about TT-Line's breaches.
"(TT-Line) has suffered substantial adverse publicity as a result of the deaths of the horses and the subsequent court proceedings," Justice Blow said.
"It seems very likely many members of the public now do not realise the deaths ... are no longer attributed to any negligence on the part of the company."
TT-Line, which is owned by the Tasmanian government, introduced visual checks in 2019 to ensure horses were individually stalled.
The driver of the horse transport truck, former Australian polo captain Andrew Williams, was fined $15,000 in 2023 after pleading guilty to animal welfare act breaches.
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