A large proportion of the fish species in New Zealand waters are in good health according to the Ministry of Fisheries.
Under the quota management system, 72 of 101 stocks surveyed are considered near or above target levels. The survey included around 70 of the most important species.
Of the 29 considered below target levels, three are highly migratory tuna species.
Other fish stocks falling below acceptable levels include one of the most valuable - hoki.
Many of those still threatened had reduced catch limit cuts on them recently, including orange roughy near the Chatham Islands and Bluenose.
West Coast North Island snapper, paua, gemfish and longfin eels are also below target levels.
The ministry says about $17 million was spent on fisheries data collection over the past year.