A proposed Threat Management Plan estimated on average 334 nationally vulnerable Hector's and two nationally critical Māui dolphins died from toxoplasmosis every year, due to cat faeces in the water.
That dwarfed the 58 NIWA estimated died in trawl or set nets. NIWA used government-observer fishery data to estimate the number of dolphin deaths through bycatch from commercial fishing.
Dolphin expert Liz Slooten said the theory was nonsense and fishing nets posed a much greater threat to dolphins than the disease spread by cats.
The man behind the theory, Jim Roberts of NIWA, said a quarter of all dolphin deaths he looked at were attributed to toxoplasmosis and it was worth further study.
An infected cat could shed about 20 million toxoplasmosis cysts, he said.
"It's not something that we typically hear about very much, but there are some things we know about the toxo parasite, which is that it's incredibly hardy and can last for about a year in sea water," Dr Roberts said.
"There is lots of research quite recently looking at vaccines for cats, so they don't shed the cyst."
However, Otago University dolphin expert Professor Slooten was surprised the theory that cats posed a greater risk to dolphins than fishing nets had even seen the light of day.
The figure of 300 dolphin deaths a year from toxoplasmosis was "wildly exaggerated" and had been based on a sample of just 28 dolphins, she said.
"So far, the only species anyone in the world is worried about in terms of toxo is seals and sea lions, the very endangered monk seal for example.
"There's no suggestion anywhere else in the world that this is a problem anywhere like the magnitude that's being suggested.
"If there really were 300 dolphins being killed each year by toxo, then not only Māui but Hector's dolphins would be free falling towards extinction," Dr Slooten said.
Only about 60 Māui dolphins and about 15,000 Hector's dolphins remain.
Conservation Minister Eugenie Sage said it was important to educate people about the impact of cats.
"It's ensuring that their faeces don't go into streams and waterways, so cat owners that keep their cats indoors can help, and things like riparian planting," Ms Sage said.
The government is proposing to significantly expand areas of ocean around New Zealand where of set nets and trawl nets will be banned to better protect the rare dolphins.https://www.geezgo.com/sps/58346
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