Up to 40 fur seal pups have been found dead near Kaikōura.
The Department of Conservation (DOC) said they were found south of Ohau Point in mid-May.
Three were sent to Massey University for necropsy.
DOC regional operations director Roy Grose said there were no signs of physical injury and based on early diagnosis, two of the pups likely died of pneumonia.
He said other factors such as biotoxins, viruses or bacterial infections had not been ruled out and pups had died because of starvation or environmental factors in the past.
DOC said it would keep monitoring the situation but the deaths were unlikely to affect the wider Kaikōura fur seal population.