A group of about 50 pilot whales were reported stranded on the beach at Port Levy on the Banks Peninsula about 6.30am.
The Department of Conservation, locals and volunteers from marine group Project Jonah helped refloat 35 whales, but more than a dozen died.
Project Jonah volunteer Mark Simpson said the whales entered the bay overnight but became disorientated and stressed.
The whales may have been caught by the tide while chasing fish, he told One News.
Local volunteer Ted Haowden (Crrct) said the whales first visited the bay last night and locals guided them back out to sea.
"We thought everything was ok, we checked them in the boat and then we woke up this morning and saw a whole lot on the beach here," he said.
"We really just stood with them and as the tide came in ... we were just able to push them out and away they went."
Mr Simpson said a mass standing was very unusual.
"In this area it's a relatively rare event although there have been mass strandings in Canterbury in the past," he said.
The dead whales will be buried on the beach on tomorrow afternoon.
