Seabirds are frequently reported as bycatch in fisheries, with most reported captures being either albatrosses or petrels.
Coastal seabirds such as shags, penguins, and gulls have also been reported as bycatch in commercial fisheries.
To monitor the impacts of fishing on these species, Government observers on fishing vessels record any protected species bycatch incidents that occur.
Observer data on protected species captures are maintained by the Ministry for Primary Industries (MPI), with identification of captured animals carried out by the Department of Conservation (DOC).
However, observers are only present on some fishing vessels, and to estimate total captures in a fishery, it was necessary to use statistical methods to extrapolate from the observed fishing to the unobserved fishing.
An analysis by Wellington-based Dragonfly Data Science has shown the "total observable captures" - an estimate of the captures that would have been reported, had observers been present on all fishing vessels.
There may have also been additional mortalities, such as birds struck by fishing gear but not brought on board the vessel, that were not recorded by observers.
These are referred to as "cryptic mortalities" and were not included in the estimates of total captures, nor was there any evaluation of potential survival of seabirds recorded as captured but subsequently released alive.
The methods Dragonfly used for the estimation followed those described in technical reports on bycatch estimation for seabirds and marine mammals.
Over the 2013-14 year, there were 512 observed captures of all birds in trawl fisheries.
These included 125 sooty shearwaters, 105 white-chinned petrel, 71 New Zealand white-capped albatross, 45 Salvin's albatross, 34 southern Buller's albatross and 39 fulmars, petrels, prions and shearwaters.
The others included flesh-footed shearwater (19), albatrosses (13), grey petrel (11), Westland petrel (9), black petrel (8), prions (7), smaller albatrosses (4), Procellaria petrels (4), storm petrels (2), short-tailed shearwater (2), northern giant petrel (2) and common diving petrel (2).
There were further cases of single catches of shearwaters, northern Buller's albatross, mid-sized petrels and shearwaters, grey-backed storm petrels, fairy prions, black-browed albatrosses, Antarctic prion, Chatham Island albatross and Buller's albatross.
Greens: stricter controls needed
The Green Party responded to the figures by calling for tougher controls on the fishing industry.
"The deaths of so many native animals as the result of the fishing industry is completely unacceptable," said the party's primary industry spokesperson Eugenie Sage.
"We don't allow hunters to accidentally kill kakapo or great spotted kiwi. We shouldn't allow the fishing industry to kill any of our dolphins, fur seals, or our endangered seabirds."
She noted that of the more than 500 birds found dead in trawl nets, 19 were flesh-footed shearwaters - one of 142 species that had recently been reclassified into a more serious conservation threat status.
"New Zealand is the seabird capital of the world with over 80 species based in our waters - we have an international responsibility to protect these species."
Sage was also alarmed to see there were 158 fur seals seen by observers in trawl nets, with the hoki and southern blue whiting fisheries responsible for most of the estimated 387 fur seals killed in trawl nets.
"All but one of the actual dolphin deaths occurred in the jack mackerel fishery which is dominated by huge foreign charter vessels.
"Dolphins shouldn't be being killed to catch jack mackerel which are often used for bait, fishmeal, and in petfood.
"The Government needs to clean up the commercial fishing industry by making sure there are observers on every boat, ensuring regular audits are done, taking stronger enforcement action, and prosecuting vessels where repeated bykill occurs."
But Seafood New Zealand chairman George Clement said reducing unwanted with seabirds, marine mammals and other aquatic life was a serious issue and "a core part of every fisher's business".
"We are doing everything possible to reduce these interactions to as close to zero as possible."
Crews underwent training and implemented mitigation devices to minimise these risks as much as possible, Clement said.
Specifically concerning seabirds, a wide range of industry-led initiatives to prevent captures had been developed, including the requirement for surface long-line fishers to use tori lines, night fishing, extra weights added to the lines to drop them quickly out of birds' reach and dyed baits to confuse the birds.
The industry had also been involved in trials to see if on-board cameras can be used to increase monitoring of captures.
"The ability to collect more information will better inform management decisions that best protect these species."
Further, the industry contributed at least $6 million each year through levies to DOC and MPI towards research on protected species and observers to monitor fishing vessels' activities.
This research measured the population trends in the different species to establish baselines and to assess the impacts of fishing on these, Clement said.
"Like other industrial accidents, interactions are not desirable but do occasionally occur and are an inherent risk we face, which is why we have plans in place to minimise these risks.
"It is important, however, to put the number of interactions into perspective.
"What is of most importance is whether numbers of interactions are causing an adverse effect on the population - which is why research is focused on measuring the species' populations and how their numbers are trending.
"This then informs whether we need to take further action."
