The whale in the Avon Heathcote Estuary died overnight.
DOC Operations Manager Andy Thompson said the whale is thought to be a fin whale about 7m long.
It stranded in standing water in the middle of the estuary near Moncks Bay and is being rolled by the tide, which may sometimes make it look like it is moving.
It is unusual for a whale to come into the estuary and we do not know why this one has done so on Sunday night.
“We intend to do a recovery operation for the remains and are currently working on a plan
“We are working closely with Te Ngāi Tūāhuriri Rūnanga, Project Jonah and the Coastguard.
“We’re asking members of the public to keep clear of the area, we do not need any assistance.
Please keep any boats, including kayaks, off the water.”