One of the authors of the critical study, Professor Liz Slooten from the University of Otago, said the majority of New Zealand fish species are managed on information directly from the fishing industry, such as self-reported catch and effort data, "without any independent science".
"Many of these fisheries are doing very poorly and causing serious environmental impacts. New Zealand is failing miserably at looking after the majority of our fish stocks for the public."
Another author, University of Otago's head of marine science Professor Steve Dawson, said "world leading spin" on the quota management system was "so often repeated that it is now earnestly believed by the majority".
"While the notion that New Zealand leads the world might promote a healthy spirit of innovation, it can also degenerate into smugness and complacency. Such complacency is rife in MPI and among politicians."
Some of the issues raised in the journal article include a failure to collect independent scientific data, that three-quarters of New Zealand fish stocks have no formal estimates of population sizes, funding for stock assessment is less than half of what it was in the early 1990s, data on ecological impacts is inadequate, widespread illegal dumping and misreporting was distorting catch statistics, and an independent review of fish dumping and dolphin by-catch "demonstrated industry capture of the regulator".
The authors argue that the claims made by the University of Washington scientists are based on an "untrustworthy" opinion survey that interviewed seven people, five of whom worked for the fishing industry, MPI or the National Institute of Water and Atmospheric Research, who do stock assessments, while the other two remained anonymous.
Dawson said the majority of the fishing quota was being "bought by a small number of companies and wealthy individuals".
"This has been bad for small-scale fishers, bad for managing fish populations and bad for protecting the marine environment."
Auckland University's Dr Glenn Simmons said fishers should be provided incentives to "use more sustainable fishing methods".
"We could ensure that all fish is brought back to shore... rather than some of it being dumped at sea, which would drive real innovation in unexpected ways."
In a statement, an MPI spokesman said they appreciate the importance of critical debate in the scientific community, "however we stand behind our scientific findings that show New Zealand's fish stocks are in good shape".
"The letter referred to... is responding to an independent scientific article that also found that New Zealand's fisheries management system is working well.
"All of New Zealand's major commercial fisheries have full stock assessments, and these assessments are all independently reviewed in a transparent and open process. To make sure our assessment methods are robust, we periodically get the world's best fisheries scientists to review our approach."
MPI said it was undertaking a programme which would strengthen its fisheries management system, called the Future of our Fisheries.
"The first stage of this programme is the integrated electronic and reporting system [IEMRS] which will put cameras and geospatial tracking on every commercial fishing vessel, and will require electronic reporting of fishing activity."
The spokesman said IEMRS would "deliver more accurate and up-to-date information for MPI to make fisheries management decisions, and is expected to act as a significant deterrent to illegal activity".
