Hundreds of penguins are likely dying in fishing nets each year, conservation group Forest & Bird says.

Photo: AFP / RICHARD ROBINSON / Cultura Creative

It said the birds, including the endangered hoiho / yellow-eyed penguin, were dying after being unintentionally snared in set nets moored close to the coast.

The group said material gathered from the Ministry for Primary Industries (MPI) under the Official Information Act showed 14 penguin deaths occurred in the year from October 2015 to October 2016, but this was just the tip of the iceberg.

Thirteen of these were reported by MPI observers but only 3 percent of boats had MPI observers onboard, so the real number of penguin deaths had to be higher, it said.

Forest & Bird chief executive Kevin Hague said this was not good news.

"It looks as if the fishing industry is killing hundreds of penguins in set net fisheries and almost none of it is being reported," he said.

That was because there was no mechanism to determine how many were dying.

'It is always dangerous to extrapolate' - MPI

However, MPI director of fisheries Dave Turner said the problem was simply not well understood enough.

"It is possible that some penguin deaths are not being reported," he said

"But we don't rely solely on reports, we do our own risk assessments and we have our own models.

"It is always dangerous to extrapolate - that is why we use scientific modelling and reports."

Mr Turner said the planned installation of cameras on fishing boats would help.

"Then we can get some real data and that will tell us what to do."

Fisheries Inshore New Zealand chief executive Jeremy Helson said his members were legally obliged to report the death of protected species and his organisation was working to make sure they did so.

"I think most fishermen do a pretty good job," Dr Helson said.

"Increased reporting is going to be something we are working on in the future."