Scottish Fisheries Minister Ross Finnie has told MPs that "community quotas" should not be allowed to replace the existing system.
The fishing industry is being scrutinised by a group of MPs
He was giving evidence to a committee which is preparing a report on the long-term future of the industry.
The prime minister's policy unit put forward the idea of community quotas.
Each fishing port would be given an area of the North Sea and an annual quota and be left to decide how, when and by whom the fish would be caught.
The scheme is a variation on the local management committees already being established by the European Union.
It is one of the ideas being considered by MPs on Westminster's environment, food and rural affairs committee.
Its members are in Scotland on a two-day fact-finding mission to gather evidence for a report into the UK's fishing industry.
During the trip they are touring fish markets and talking to fish processors, as well as representatives of the Royal Society and the Sea Fish Industry Authority.
Speaking in Edinburgh, Mr Finnie told MPs that he did not see how community quotas could replace the system of quotas organised through the fish producers associations, except perhaps in the case of distinct communities like Orkney and Shetland.
The MPs, who are due to submit their report next month, are scheduled to visit Aberdeen and Peterhead on Tuesday.