The Scottish Government is under pressure to scrap plans to shut off large areas of the waters around the Western Isles to fishermen.
The local authority had claimed that the imposition of marine designations would be “totally unacceptable” and have an adverse impact on the economy.
A marine protected area network is designed to protect sea life, habitats and the sea bed.
Councillors made the claims in a statement following a meeting in Stornoway with Scottish Natural Heritage and Marine Scotland representatives.
A spokesman for the Scottish Government said it had obligations to protect the marine environment under European law but no final decisions had been taken.
Alasdair Macleod, chairman of Western Isles Council’s sustainable development committee, said: “We are fundamentally opposed to designations being imposed on local communities by the Scottish Government and the European Union.
“The fishing industry in the Western isles is totally against these plans which will have a negative impact on the fishing industry and the general economy of the islands, particularly in Uist and Barra.
“The council is entirely supportive of the fishing industry and it is hugely disappointing that local views are just not being listened to.”
Mr Macleod said the council believed there should be a 10-year moratorium on any new designations in the Western Isles.
“I would now call on the government to respect local opinion, reverse these proposals and stand up for the Islands, the local economy and our communities,” he added.
The government spokesman said SNP ministers had obligations under national and European legislation to “protect the marine environment”.
“Particular locations are selected because they host nationally important species populations or proportions of habitat,” he added.
“Under European case law, designations under the EU habitats and wild birds directives can only take scientific evidence into account.
“Scottish ministers have not yet considered the merits of the scientific cases for these new proposals.
“Discussions with local authorities and other stakeholders will continue before, during, and after any public consultation.”