A Massey University scientist says Forest & Bird's best fish guide proves the quota management system is not working for all species.
The environmental group's consumer guide is based on a thorough ecological assessment of 78 commercial species.
The guide, to be released this week, rates bluecod, rock lobster and kahawai as good meal choices, however popular fish, snapper, orange roughy and hoki rate poorly.
The Seafood Industry Council has dismissed the guide as a campaign document, saying all fish caught under the quota management system are done so sustainably.
But Mike Joy, a senior lecturer at Massey University, says the ecological assessment takes into account factors such as bycatch and methods of fishing.