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Emergency services responded to a mayday call from an 11-metre yacht sinking near The Brothers/Ngāwhatu Kai-ponu islands about noon on Saturday.
The three people on board were found uninjured by another yacht, then put on a Coastguard Marlborough boat and taken to Picton to recover, leaving behind their "submerged, unlit wreck".
Marlborough harbourmaster Luke Grogan said their yacht had become a "floating hazard" and a "highly dangerous" threat to other vessels.
"It had submerged, but part of the structure was poking out of the water," Grogan said on Tuesday.
Authorities lost track of the drifting wreck until a commercial fishing boat struck it about 16km away at 10pm, near Cape Jackson, tearing a hole in its hull.
Police search and rescue co-ordinator and Blenheim senior sergeant Peter Payne said Coastguard Marlborough delivered a pump to the fishing boat so it could remove the water it had taken on.
"They [the fishing boat] made it back to Picton on their own steam. They weren't in any distress," Payne said yesterday.
The shipwreck then drifted towards Transpower's underwater electricity and telecommunications cables in Cook Strait, which provides electricity between the north and south islands.
Police said the yacht started sinking because it had sprung a sudden leak, but they weren't sure what had caused the leak.
Alert messages were sent out on New Zealand's marine distress radio channel when the yacht started sinking, with another round broadcast to Marlborough's marine channels once authorities confirmed it had moved into Tōtaranui/Queen Charlotte Sound.
An alert published on the Marlborough District Council website described the "submerged, unlit wreck" as a "significant hazard".
A KiwiRail spokesman said the company was aware of the warnings, but that the Tōtaranui/Queen Charlotte Sound entrance was not the usual entrance for the Interislander ferries.
The wreck did not disrupt any of the Interislander ferries.
A statement from Transpower showed another vessel threatened the nation's inter-island power cables last month after it sank 12km from the Strait's Cable Protection Zone.
The former fishing vessel Antonia, from Australia, was being towed from Wellington to Picton when it began taking on water.
Transpower was asked what caused that vessel to sink and whether people were on board, but did not respond in time.
It was the Antonia's second run-in in the Cable Protection Zone, where fishing and anchoring is illegal. It had to be towed from the zone in 2007 after running out of fuel during a voyage.
"This will be her final voyage as she will remain on the seabed with no requirement to retrieve the vessel," the Transpower statement said.
By Chloe Ranford
Local Democracy Reporter based in Marlborough