Measures to conserve the tiny fish are to be introduced next year in a bid to halt the decline in seabird numbers.
A wide range of birds, including puffins, razorbills, shags, guillemots and kittiwakes, feed on shoals of sandeel around the coast, especially in the summer months.
But declining seabird numbers have been linked with over-fishing and the possible impact of climate change on their staple food.
In a bid to tackle the problem, the Scottish Government's Marine Scotland agency is planning to include the sandeel in a new network of Marine Protected Areas, where measures to limit fishing are expected to be imposed.
The move could see an end to industrial-scale fishing for sandeels, which are used in fishmeal feed and fertiliser, in those areas.
Scottish Environment Minister Paul Wheelhouse said: "The factors that are causing seabird declines are complex and may be a result of changes in food availability, climate change and the effects of non-native species.
"We are taking action to increase protection for our important seabird populations.
"A significant programme is under way to develop a network of Marine Protected Areas [MPAs], which includes seabirds.
"MPA proposals being developed that directly help seabirds include areas for black guillemot and for the protection of the sandeel, a key food source that supports many seabird species."
A report earlier this month from Scottish Natural Heritage showed that Scotland's seabird numbers have declined over the last 25 years.
From 1986 to 2011, the number of seabirds breeding in Scotland has dropped by around 53%.
The number of Arctic skua fell 74%; Arctic tern by 72%; and black-legged kittiwake 66%. Of 11 species studied, the populations of only two, the black guillemot and the northern fulmar, have remained stable.
Sandeels, which are not true eels, are fished for off the Western and Northern Isles and in the Firth of Forth, though voluntary reductions in catches operate in some areas.
The move to protect the sandeel was welcomed by Scottish Natural Heritage, which is advising the Government on where to introduce MPAs next year.
SNH scientist Dr Greg Mudge said: "The decline in numbers and breeding success of seabirds are big issues and both are related to food supplies. Sandeels are a big source of food.
"There are changes to what is happening with sandeels. It seems it is partly down to fishing and partly down to climate-change effects on the marine environment. If it is mainly climatic there is not a lot we can do. If it is fisheries-related we can do something."
A Scottish Government spokesman said: "Marine Protected Areas proposals relating to sandeel are under development and would intend to provide added protection – over and above existing fisheries measures. Such MPAs would aim to protect sandeel and their habitat from human activities that may be damaging.
"The reasons for decline in sandeel aren't clear but may be related to climate change, for example a rise in sea temperatures.
"That's why Marine Scotland are taking forward the research project to examine the causes."
l Sandeels are small, eel-like fish which swim in large shoals and are an abundant and important part of the food chain in the North Atlantic.
l They live for less than 10 years and are 4cm to 5cm in length, but can reach 10cm.
l Their preferred habitat is the seabed, where they burrow in sand to escape predators.
l Five species of sandeels inhabit the North Sea with the lesser sandeel (Ammodytes marinus) the most abundant, making up over 90% of sandeel fishery catches.
l They are important prey for seabirds and fish, including most species of white fish.
l They support the largest fishery in the North Sea, with recent annual landings of around one million tonnes.
l The magnitude of the fishery has led to concern about the impact of sandeel harvesting on the North Sea ecosystem.
l Small sandeel fisheries operate off Shetland and the west coast and are different to the large North Sea fishery as they are restricted to small inshore grounds and managed nationally.