The population of the distinctive seabird fell 20% in the three years to 2012, according to figures.
The Shetland Oil Terminal Environment Advisory Group (SOTEAG) found there were 5782 birds around 80% of Shetland's coastline in 2009. A follow-up survey covering 90% of the coast found just 4627 birds in 2012.
Martin Heubeck, of SOTEAG, said the cause was unknown but could involve the local mussel farming industry or killer whales.
He said: "A lot of people would say that duckling predation by skuas and gulls has been severe, but it's been the case for a long time.
"Predator nets have been set at both mussel farms and salmon farms, one mussel farmer actually reported that anti predator nets were drowning eiders, but the scale and the extent of it is really a big question mark."