Otago Regional Council compliance manager Tami Sargeant said the Macandrew Bay boat shed became dislodged from its foundations and fell into the harbour.
With a cold, windy front on the way, the council was urgently asking boat shed owners to check their structures were secure, she said.
The wind combined with a king tide, an exceptionally large tide following a full moon when it is closest to Earth.
The full moon occurred on Monday.
Mrs Sargeant said it was unclear how the collapse occurred, however, the council understood another boat shed in the area might be threatened.