The 12m to 15m long, concrete hull sailing yacht came off its mooring and sank sometime between Wednesday evening and Thursday morning.
The boat is owned by Oamaru man Mike Harris.
"It came off its mooring. I don’t know why or what happened," Mr Harris said.
Waitaki District Council property manager Grant Rhodes said Mr Harris had attempted to refloat the yacht on Thursday night but was unsuccessful.
Mr Rhodes confirmed it had not been established how the vessel came adrift.
He said the tide then pushed the yacht into the southwestern corner of the harbour.
"I imagine it would’ve hit the rocks ... because it’s actually quite shallow there," Mr Rhodes said.
Yesterday, Mr Harris said he would try again to refloat the Black Crow.
"Next low tide, get the pumps on board and get it upright and go from there."
If successfully refloated, the yacht would be towed to Normanby wharf for repairs.
Some of the cabin and other pieces of the yacht had broken off, but the debris was salvaged.
Otago Regional Council harbourmaster Steve Rushbrook said the yacht was not in a dangerous position for navigation and was not causing any pollution.
"It’s not interfering with other traffic, so I’m content with that," Mr Rushbrook said.
"I’m also content there’s no pollution coming from it."
Mr Rhodes said because the boat posed no contamination issues, the mid-winter harbour swim scheduled for tomorrow, and would go ahead as planned.