Instead, law professors Meinhard Doelle and Bill Lahey of Dalhousie University in Halifax recommend shaping an industry that has a low impact on the environment and a high economic value.
"Nova Scotia's economy calls for a policy approach that addresses the risks through responsible development and robust regulation rather than prohibition," says the report released Tuesday.
But the report says fish farming should only be allowed in coastal waters that are suitable and goes on to recommend a classification system of areas that are generally suitable for the industry, those that have potential but are not ideal, and areas that are generally unsuitable for fish farms.
The classification of an area would determine how licence applications are evaluated and the likelihood of their approval. It would also play a central role in determining the terms and conditions of a licence.
The report says its findings are based on the available science and addresses "legitimate concerns" by environmentalists and some community groups without shutting down the industry.
The report was welcomed by the Halifax-based Ecology Action Centre, although spokesman Raymond Plourde said he was disappointed it doesn't call for in-water, open net farming pens to be phased out.
"We believe it is a fundamentally flawed model," said Plourde, whose group would rather see farming in closed pens or in land-based tanks to decrease pollution from fish waste.
He warned against the government "cherry picking" recommendations, saying the report needs to be adopted in its entirety to be effective.
The report says responsibility for administering environmental monitoring should be moved to the Environment Department because right now, the Fisheries Department promotes and regulates the industry, which has created a lack of trust among critics.
Under the recommended changes, the fisheries minister or an independent board would also have the power to revoke licences if a site is found to be unsuitable or is not being operated responsibly.
There is also a call for a standing regulatory advisory committee composed of representatives from the aquaculture industry and environmental groups. Coastal communities, municipalities and the Mi'kmaq would also be part of the committee.
The report also says the protection of wild salmon populations should be set in legislation as one of the criteria to be considered in leasing and licensing decisions.
Fisheries and Aquaculture Minister Keith Colwell said it would take months for the government to review the feasibility of all the recommendations.
Doelle and Lahey, who couldn't be reached for comment, were appointed in April 2013 by the former NDP government. The panel's consultations included 42 community meetings and over 20 meetings with organizations and individuals.