However, RSPB Scotland and the Whale and Dolphin Conservation Society (WDCS) are furious because they claim seabirds and cetaceans have been neglected in the process.
Although more than 30 Marine Protected Areas (MPAs) have been proposed, none focus on whales and dolphins, and only one species of seabird is included – the black guillemot.
Rory Crawford, seabird policy officer at RSPB Scotland, said after spending a decade campaigning for the Marine (Scotland) Act, he was disappointed and angry.
Six MPAs were proposed by RSPB Scotland to protect seabirds, but all have been rejected.
“It was a huge success story for us after a decade of campaigning to get the Marine (Scotland) Act, but now seabirds, whales and dolphins have been marginalised,” said Mr Crawford.
A list of MPAs is being drawn up and will be presented to the Scottish Parliament by the end of the year, and will be open for public consultation in 2013.
Sarah Dolman, head of policy for Scotland at WDCS, was furious to discover none of the MPAs on the list included any whale or dolphin species.
“We are very angry and very disappointed because ultimately we want a network that Scotland can be proud of. We want people to come and visit and enjoy these species. These are milestone species for Scotland and not including them just seems ridiculous.”
Ms Dolman said they provided plenty of evidence to the Scottish Government to support inclusion of the five MPAs, but they were told not enough research had been done and decisions on those sites was being postponed indefinitely.
Read full story: Scotsman.com by Jenny Fyall