Hatton Bank, one of the areas proposed by the Scottish Government as a Special Area of Conservation (SAC), is 310 miles to the west of Lewis and more than 10 times the size of Fife.
The areas have been submitted to the EU for consideration, but Scottish fishermen are challenging the boundaries of one.
Officials are stressing that there will be no fishing ban, although there may have to be negotiated controls.
The five proposed SACs are between the 12-mile limit of UK territorial waters and the edge of the UK Continental Shelf designated area.
They do not include a controversial proposal for an inshore SAC in the waters near Barra. The new offshore SACs range from three locations far out into the Atlantic west of the Outer Isles to one 12.5 miles east of Shetland and another 31 miles north of Cape Wrath.
Rural Affairs Secretary Richard Lochhead said: "Scotland's seas provide rich and diverse ecosystems that are home to a wide array of plants and animals, including internationally important species.
"It's our duty to protect this precious environment, and these five SAC designations are a big step towards our commitments under the international Marine Protected Area networks. The Scottish Government and the Joint Nature Conservation Committee have carried out extensive and productive engagement with stakeholders – including the fishing industry – before these proposals were submitted.
"We will continue dialogue with stakeholders to ensure that any future management measures are well-designed and appropriate."
Marcus Yeo, chief executive of the Joint Nature Conservation Committee, the UK's statutory nature conservation body, said: "This landmark submission of marine SACs means that over a twelfth of UK seas are now within Marine Protected Areas, and is a major step forward in the conservation of our precious sea life.
"These sites will protect substantial areas of colourful bedrock, stony and coldwater coral reefs. People think that coral reefs are only found in exotic, tropical locations and don't realise that we have these fragile habitats right here on our doorstep as well."
Bertie Armstrong, chief executive of the Scottish Fishermen's Federation (SFF), said the body supported the process of sensible protection and, as the principal stakeholder, would continue to engage in the process.
"However, in some of the areas, particularly the East Rockall Bank, the boundaries are incorrect," he said. "This has led to the inclusion in the Government proposal of areas where there are no notable marine features. This is disappointing, but the crunch time for us will come when practical management measures and restrictions are set."
Calum Duncan, programme manager of the Marine Conservation Society Scotland, said: "We are delighted with today's announcement confirming designation of five new European sites.
"They must help protect fragile coldwater corals, soft corals, sponges, deepwater brittlestars and other sea life in Scotland's deeper waters."