The female was one of four yellow-eyed penguins (hoiho) bycaught by inshore trawlers since on-board cameras on commercial fishing vessels were introduced on October 31 last year.
Yellow-Eyed Penguin Trust Te Tautiaki Hoiho conservation science adviser Dr Trudi Webster said losing a breeding female was "really catastrophic" for local populations of northern hoiho around the mainland and Stewart Island (Rakiura).
"They have the biggest long-term effects on the hoiho population, so that means you miss out on potential breeding birds."
She said the northern population was down to about 160 breeding pairs — a decline of 78% in the past 15 years.
Dr Webster said while conservationists provided supplementary food and rehabilitation to injured hoiho to help the species survive, things were not looking "particularly rosy" for the long-term survival of the species.
She said while there were no overnight solutions to problems caused by climate change, removing setnets from the bird’s habitat or managing how those setnets were used would be an effective strategy.
Forest & Bird Otago Southland regional conservation manager Chelsea McGaw said setnets, also referred to as "gill nets" were long nets similar to those that go on a tennis court that sunk to the bottom of the water and hoiho would get stuck in them and drown while they were foraging for fish to eat.
She said regulations for commercial fishermen to night-set and avoid day-setting would help work around the hoiho behaviour patterns.
It was quite sobering for her to find out about the last breeding-aged female to be caught at Sandfly Bay.
"Even the loss of one hoiho in such a dwindling population is a big knock back and for this to be a breeding female it’s even worse."
Conservation biologist Dr Rachel Hickcox said marine protection for hoiho was "woefully inadequate".
She said bycatch was one of the many critical threats hoiho faced including starvation, disease and human disturbance.
To protect hoiho the southeast marine protected areas network needed to be immediately and officially designated.
However, even with the network of protected areas — including six newly approved marine reserves — only about 3.6% of the birds’ foraging range would be protected, she said.
She recommended consistent, widespread surveillance of reserves and increased enforcement and penalties for non-compliance.
"We need to understand how fisheries are indirectly affecting hoiho — overfishing and seafloor destruction.
"An ecosystem-based fisheries management approach is required that puts the protection of the entire marine environment above that of commercial gain."
