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The New Zealand-flagged trawler Remus ran aground at Big Bay, 40km north of Milford Sound, about 10am on Thursday.
Rescue Coordination Centre New Zealand (RCCNZ) was alerted but no distress call was made, and no search and rescue action was taken.
There were no reports of injuries to the four crew members on board.
Insurers and a salvage team reached the site on Friday. It is understood the vessel may have suffered mechanical issues.
No oil was spilt into the marine environment.
A vessel from Westport was enlisted to try and tow it off the beach at high tide over the weekend.
However, Southland harbourmaster Lyndon Cleaver said it was a tricky operation.
The shallow approach to the beach meant the tow vessel could only get to within about 1000m of the Remus.
But around 1am on Monday, they managed to get the heavy, steel-constructed trawler refloated.
"There were a few minor hiccups the day before but everything went according to plan," Cleaver said.
"It certainly wasn't an easy task and had to be thought through."
The vessel is now making its way to Nelson where it will be thoroughly checked over.
The crew are all safe, Cleaver says.
"At the end of the day, it was a good outcome for all – the vessel, the crew and also for the environment," he said.
"This was the best outcome – and thankfully, the weather played the game."
Maritime New Zealand is still investigating.