Don Thompson, president of the Jersey Fishermen's Association, said quotas meant some boats were out of the water for three months of the year.
The European Union (EU) has published new quotas for 2015 onwards, which include a ban on discarding certain species.
Marine officer Greg Morel says local fishermen are bound by EU agreements.
He said: "There are some things discussed in Brussels that will have an impact on local fishermen because we have an agreement around managing our seas jointly."
Mr Thompson said the existing system was not working as it did not take in to consideration local fish stocks.
He said: "If we don't do something we are going to be deprived of the ability and right to catch fish in the waters around this island. That is unthinkable.
"There are lines in our fisheries management agreement that bind us to Europe - and that will always be there - but that doesn't stop us working on a scientifically backed system that moves away from quota stocks."
Mr Thompson said the announcement on Tuesday by EU ministers over the recent quota changes "could have been worse".
He said it was still not good news as quotas were still dropping but at the same time stocks were improving, especially in island waters.
He said: "We've had four years of a total ban on Undulate Ray. We put forward a specific request to have that lifted because stocks in Channel Islands waters are fine, they are plentiful.
"But because they have suffered from over fishing in Portugal and Ireland, there is a complete ban."
The meeting is on Wednesday evening and Mr Thompson said he did not expect any immediate outcome.
Jersey fishermen are to meet with ministers to propose alternatives to the current quota system.