If the bight is a foraging ground for them it will be the fifth known such area south of the equator and an important place for them to gain energy stores to survive and breed. Activities like offshore oil drilling could affect their well-being.
All blue whales have been extensively hunted, and their numbers are depleted.
Pygmy blue whales are a southern hemisphere species that live in the Indian and southern Pacific oceans and breed in the Indian and south Atlantic oceans. The whales are known to migrate up the west coast of Australia from Perth to Indonesia.
Dr Torres would like to know where they migrate locally.
"We are not sure of their migration patterns. We hope to find this out eventually."
Her team has set five hydrophones in the water, from north of Cook Strait to west of Cape Egmont. They will record whale calls and provide information about whale movements.
While surveying the bight those aboard the Ikatere have seen other marine mammals - pilot whales, fur seals and common dolphins.
Early Europeans called the bight Mothering Bay, because mother whales calved there. Dr Torres said those whales would have been southern right whales.