Ministers are asking for a second opinion on the proposal to make the Sound of Barra a special area of conservation (SAC), despite watchdog Scottish Natural Heritage (SNH) recommending the move.
The project is designed to protect harbour seals, sandbanks and reef habitat. Now the scientific case for change will have to be proved.
SNH's advice has been received by Environment Minister Paul Wheelhouse, alongside a report on the public consultation exercise, but there have been hundreds of objections, many of them from Barra, expressing deep concern the SAC designation would restrict fishing, particularly for shellfish, as well as prejudice renewable energy development.
The objectors have not been placated by SNH, which says fishing could continue on a managed basis. One previous minister admitted that "relations between SNH and the local people [of Barra] have broken down". It didn't help that, in August last year, the Scottish Government approved plans to designate an area of seabed off East Mingulay, also near Barra, as a new SAC.
At one point the Sound of Barra SAC was to have included the island's famous beach runway, but the area has subsequently been redrawn.
The independent expert review of the scientific case for designation is expected to be completed before the end of this year.
Mr Wheelhouse said: "The Sound of Barra is home to important colonies of common seals as well as reefs and sandbanks that support many species. That's why we are considering taking steps to designate the area as an SAC.
"However, the proposed SAC has resulted in a wide range of views, some of which take issue with the scientific assessments carried out. So that I have a complete picture on which to base my decision, I've asked for an independent review of the scientific case to be completed."
He thanked SNH for the comprehensive case the agency had prepared.
He said his final decision would be based on sound science, and added: "I can assure the communities involved that if I choose to designate, we will ensure the right balance will be reached between environmental conservation and their social, economic and cultural requirements."
In February, island fishermen demonstrated outside the Scottish Parliament on the day Highlands and Islands Tory MSP Jamie McGrigor led a backbench debate on the issue at Holyrood.
At the same time, Rory MacNeil, chief of Clan MacNeil of Barra, accused SNH and ministers of not listening to the islanders. Campaign group Southern Hebrides Against Marine Environmental Designations (Shamed) was set up in 2009 to fight both the East Mingulay and the Sound of Barra SACs.
Its chairman, crofter-fisherman Angus MacLeod, talked to The Herald from a trawler in the North Minch. He said: "It's good news. It is what we have been calling out for a very long time."
He said there were a lot of questions to be answered.
"For example, how can they say they want to designate the area to protect seals, yet SNH has allowed a large multinational company to set up a salmon farm within the area and issued a licence to shoot seals? It doesn't make sense," he added.
SNH accepted there were wider concerns about the proposal but insisted: "We advise on the scientific case for designation, and have provided a robust report that will meet the concerns raised in the European Commission's moderation process."