This article from The Age (a Melbourne newspaper) provides more detail. It would seem that they weren't actually observed in the act of fishing in Aussie waters.
Fishermen caught in epic chase acquitted
November 5, 2005 - 5:44PM
Five foreign fishermen have been acquitted of poaching Australian fish stocks in a case that involved the world's longest sea chase and cost the government millions of dollars.
A District Court jury in Perth has found the men not guilty of illegal fishing charges two years after their arrest at the end of the 7,000km pursuit across the Southern Ocean.
Their acquittal is an embarrassing setback for the Australian government as it tries to stop illegal operators plundering prized stocks of Patagonian toothfish in sub-Antarctic waters.
It was the second time the crew of the Uruguayan-registered ship Viarsa 1 had stood trial after a jury failed to reach a verdict last December.
The men, who are from Uruguay, Spain and Chile, have been living in a merchant seamen's hostel in Fremantle for two years and are expected to be repatriated in the next few days.
"It's good news. Obviously they're very emotional because they're going to return to their homelands and they've been away from their families for two years," the men's lawyer Mark Trowell said.
Federal Fisheries Minister Ian Macdonald expressed disbelief at the verdict.
"I am amazed at the decision," he said.
"Notwithstanding the decision, I have no regrets over the incident.
"I would repeat the exercise tomorrow if a foreign fishing vessel is sighted by an Australian patrol vessel inside the Australian Fishing Zone (AFZ)."
Viarsa's Uruguayan captain Ricardo Mario Ribot Cabrera, 58, Spanish first mate Antonio Garcia Perez, 40, officers Francisco Fernandez Olveira, 40, Jose Gonzalez Perez, 38 - also of Spain - and Chilean crewman Roberto Enrique Reyes Guerrero all pleaded not guilty to intentionally using a foreign vessel for commercial operations in the AFZ.
Cabrera and Garcia Perez also denied one count of intentionally having in their charge a foreign boat equipped for fishing inside the zone.
The men were charged following the three-week pursuit begun by an Australian fisheries vessel around Heard and McDonald islands on August 7, 2003, and continued for 7,000km through the mountainous seas of the Southern Ocean.
The chase only ended when armed South African Fisheries officers and security guards boarded the Viarsa with assistance from a South African tug and a British fisheries patrol boat.
The West Australian District Court trial was told Viarsa had almost 97 tonnes of toothfish on board, along with 92 tonnes of bait and hundreds of boxes of fish products when it was finally inspected.
The chase and subsequent prosecution have cost the federal government at least $4.5 million, according to information tabled in the Senate by the government in August.
Some of that money was recovered when the government auctioned the Viarsa's catch for $1.9 million.
Mr Trowell said the Viarsa was never caught with fishing gear in the water and the captain was under orders from Uruguay not to stop once the pursuit began.
"At the end of the day they just didn't have the evidence," he said.
The men would have faced hefty fines if convicted, but people found guilty of illegal fishing cannot be jailed under an international convention observed by Australia.
The pursuit of the Viarsa prompted the government to step up operations against poachers in the Southern Ocean with the addition of the armed fisheries vessel Ocean Viking to patrol the region.
The Viarsa, a trawler worth about $US5 million ($A6.77 million), remains impounded at a shipyard south of Fremantle.
Its Uruguayan owners are continuing action in the Federal Court in Perth in an attempt to recover the ship and be reimbursed for the lost toothfish catch.