The whale was being left to decompose because the site was difficult to access by land or water, which meant it was impractical to remove or bury the carcass.
Surfers and swimmers should be aware that thee carcass also increased the risk of shark encounters in the wider area, such as at Warrington Beach and nearby surf breaks.
"While we have not seen any evidence of increased shark activity in the area, research has shown that sharks may remain near beached whale carcasses in search of food," Fyfe said.
The department and Kati Huirapa Rūnaka ki Puketeraki, the local rūnaka, would monitor the decomposition of the whale, which could take several months.
Department staff would be meeting with the Warrington Surf Life Saving Club to discuss the risks in the lead-up to summer.
A DNA sample was taken from the whale and the cause of death was not known, Fyfe said.
Humpback whales could be found off the Otago coast between May and July as they migrate north away from the cold Antarctic waters. However, it was unusual for them to wash up.