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On Monday, 49 long-finned pilot whales stranded at the remote beach at the top of the South Island - and a number died.
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The following day a group of about 28 came ashore again.
A search along the section of the inner Spit accessible to vehicles and a check of the nearby beaches failed to find any live whales, the Department of Conservation said.
A DOC spokesperson said it was hoped the pilot whales that spent yesterday swimming offshore from Farewell Spit had made their way out to sea.
Dead whales from the stranding are on the Spit and several were on other beaches.
Rangers are working to move the dead whales to a pit in an area of Farewell Spit away from public use.
Manawhenua ki Mohua iwi representatives will say a karakia for the dead whales.