Mr McCully said the program's justification of providing scientific research was "highly dubious".
He said the aging whaling fleet was increasingly reliant on Japanese government support, as there was little demand for whale meat from Japanese consumers.
"The whaling programme serves no useful purpose and deserves to be consigned to history."
The last whaling mission to the Southern Ocean was abandoned in February after whalers were hindered by the Sea Shepherd conservation society.
Extra security is expected to accompany the whalers as they deal with expected fierce opposition from the group.
Sea Shepherd has named its anti-whaling mission Operation Divine Wind. 'Divine wind' is the English translation of the Japanese word 'kamikaze'.
Sea Shepherd captain Paul Watson said the name meant the society was calling upon the 'divine wind' to protect the whales from the cruelty and criminally lethal activities of the Japanese whalers.
Labour and the Green Party said the situation in the Southern Ocean was increasingly dangerous and called for New Zealand navy vessels to be sent to the to monitor the Japanese whaling fleet.
Labour conservation spokeswoman Ruth Dyson said the vessels could help to send the "strongest possible message" of opposition to the Japanese Government.
"New Zealanders don't like sitting on the side-lines when bad things are happening. We want to be part of any action to stop the slaughter of whales."
Green Party oceans spokesperson Gareth Hughes said the navy could act as an independent observer of the whale hunt to document the "slaughter" and ensure the safety of the Sea Shepherd protest vessels.
"Diplomacy alone will not secure the protection of whales.
"As last year's clash between the Ady Gill protest boat and a Japanese whaler demonstrated, there is a very high potential for things to go wrong on the hunt. It is an extremely hostile natural environment and human emotions are running high."
Mr McCully urged Sea Shepherd and the whalers not to put their lives, or the lives of others, at risk.