Inshore commercial fishermen say the high price they are paying to quota owners will eventually squeeze many out of business.
The Quota Management System was introduced 20 years ago to ensure sustainable fishing and stop key stocks from being plundered.
But inshore fishermen now say the system is turning them into an endangered species.
Fisheries giants Sanford, Sealord, Talleys and Aotearoa Fisheries own 80% of quota rights, with the remainder owned by smaller companies.
Others have to lease quota rights and pay annual catch entitlement fees that can account for two-thirds of the price they get for a kilogram of fish.
The Federation of Commercial Fishermen says when the total allowable commercial catch for a species such as snapper is reduced, its deemed value increases and there is very little profit for fishermen who lease quota rights.
President Doug Saunders-Loader says the way the Government sets the deemed value of a fished species is a problem.
"You're talking about fish that is being purchased at a particular price and deemed values are unfortunately being set on that price, as opposed to what price that fish is being landed at.
"Deemed values unfortunately follow market prices and as a consequence of that the port price for the fishermen becomes secondary."