The animals—also known as "hoiho" in Māori—are known as the world's rarest penguins and are only found in New Zealand.
Only 14 nests were found on the island compared to 24 last year, the survey from the Department of Conservation revealed. Since the island is predator-free with limited human access, terrestrial influences are unlikely to be the cause, the department pointed out.
Forest & Bird, a Wellington-based conservation nonprofit, is blaming the commercial fishing industry for the loss, suggesting that the animals were most likely caught and drowned in the nets of fishing trawlers.
"Unlike previous years where disease and high temperatures caused deaths on land, this year birds have disappeared at sea," said Forest & Bird chief executive Kevin Hague in a statement. "There is an active set net fishery within the penguins' Whenua Hou foraging ground, and the indications are that nearly half the Whenua Hou hoiho population has been drowned in one or more of these nets."
Only three percent of the commercial trawlers had official observers onboard to report penguin deaths. Incidentally, Forest & Bird noted that all the recorded deaths came from the small percentage of boats that did have observers.
"It's simply unbelievable that almost every penguin killed in the set net fishery was killed on a boat that had an official observer onboard," Hague said. "As a first step, [the Ministry of Primary Industries, which oversees the fishing industry] needs to get more of their observers onto set net vessels and prioritize putting cameras on set netting boats."
"Responsible set netters need to ask the question of their fellow fishers—why is it that the only recorded by-kill of penguins appears to be on monitored fishing vessels?" he asked.
The environmental group is urging government action and for the fishing industry to agree an immediate set of actions to eliminate the risks from set netting in the penguins' feeding areas.
"We are asking [the Department of Conservation] and [the Ministry of Primary Industries] what they intend to do to save our hoiho from extinction, because at current rates of decline we are on track to lose hoiho completely from mainland New Zealand. We have also written to the Minister of Conservation, expressing our concern," Hague said.
"This bird is so special that it appears on New Zealand's five dollar note," Hague said. "The critical information about the Whenua Hou catastrophe should not have been held back from the public. Instead we need honest conversation with New Zealanders spelling out the actions that will be taken to prevent it happening again."
The yellow-eyed penguin is not faring any better elsewhere in the country. According to the Guardian, there are just 1,600 to 1,800 of these penguins left in the wild, down from nearly 7,000 in 2000. They face wide-ranging threats from climate change to disease.
"While nest numbers are similar to last year from Dunedin northwards, there are declines further south," said Department of Conservation Threatened Species ambassador Nicola Toki. "The estimate for the total southern east coast based on current counts is around 250 nests, down from 261 a year ago. This number is of concern given historically there were between 400-600 breeding pairs and the current number is the lowest for 27 years."