Breeding pairs of yellow-eyed penguins are down by nearly half along the Otago/Southland coastline and research is ongoing into why many of the adult birds are dying.
The Department of Conservation estimate there are 250 breeding pairs of the penguins, or hoiho, as their breeding season comes to an end.
It is similar numbers to previous years but lower than historically, when there have been between 400 and 600 breeding pairs.
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The monitoring identified some regular issues for the nationally endangered penguins, such as avian diphtheria in chicks and predation injuries at sea, DoC's Coastal Otago operations manager Annie Wallace says.
"Like last season, this year there have been some unexplained adult deaths," she said.
"Further investigation into these deaths indicate signs and symptoms which are consistent with previous events. In 2013, 67 hoiho were found dead and in 2017 six were confirmed to have died, all in similar circumstances."
Despite research into the reasons for these deaths - which includes sending samples to Wildbase at Massey University - and the ruling out of many possibilities, the exact cause has not yet been identified, she said.