The pioneering eradication of brown rats, using brodifacoum in poison baits, was carried out by the New Zealand Department of Conservation (DOC) in May and June 1988 following the success of a pilot campaign on the adjacent, and much smaller (9 ha or 22 acres), Hāwea Island in 1986. Breaksea is six times the size of the previous largest island on which rat eradication had been successful. Since then, DOC has overseen the eradication of a suite of introduced animals from several other islands, the largest being Campbell Island at 113 km2 (44 sq mi).
Fiordland crested penguins breed on Breaksea. Since rat eradication various threatened species of New Zealand's native fauna have been introduced, or reintroduced, there. These include the tieke (saddleback), mōhua (yellowhead), Fiordland skink and knobbled weevils.