The great skua has seen a significant drop in its breeding population, with the Hermaness Nature reserve alone seeing a worrying 90 per cent fall.
That is the warning from NatureScot, which has temporarily suspended ringing and research activities to minimise unnecessary disturbance.
It comes amid warnings of some seabird species returning to Scotland in lower numbers this season following the devastating outbreak of avian flu last year.
Despite recent outbreaks in England, NatureScot says there is cautious optimism that colonies in Scotland have so far avoided the high number of deaths observed last summer.
However, the great skuas – or bonxies – have been especially hard hit.
Wildlife manager Alastair MacGugan said: “It is too soon to draw firm conclusions about the impact of last year’s terrible losses, but the low numbers of great skua and terns returning to our shores is certainly concerning and something we are keeping a very close watch on.
“The good news is that, in Scotland at least, we are not seeing the large numbers of dead birds around breeding sites that we did last year.
“This may mean that the remaining birds have gained some level of immunity to the virus. If so, then there is cause for optimism as populations may begin to slowly replace the losses that occurred last year.
“This is far from the end of the outbreak, however, and we are certainly not complacent.
“We may see the virus switch to other species in the future, as has happened with the gulls elsewhere in the UK.”