The seven-metre (23-foot) fin whale died in the early hours after beaching on an estuary sandbank near the Christchurch suburb of Moncks Bay, the conservation department said.
The coast guard used an earthmover to lift the whale's body out of the water.
A crowd of people perched on boulders at the edge of the beach, some taking pictures of the scene.
"A lot of people are concerned. Whales are quite a point of fascination for people, especially a whale this big being so close to the city," Daren Grover of conservation group Project Jonah told Radio New Zealand.
Fin whales can grow up to 26 metres (85 feet) long and weigh up to 80 tonnes.
Conservationists have recorded more than 5,000 whale strandings in New Zealand since 1840 but they rarely swim so close to Christchurch.
"It is unusual for a whale to come into the estuary and we do not know why this one has done so," conservation department operations manager Andy Thompson said.
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