Corncrakes are among species dependent on machair
Planned cuts to missile test ranges staff on the Western Isles could have a knock-on effect on wildlife habitat, RSPB Scotland have said.
Some of those employed on Benbecula and South Uist also run crofts and farm fertile grasslands, known as machair, using traditional methods.
RSPB warden Jamie Boyle said the machair was key to the survival of rare species such as corncrake.
He said if the crofting stopped, the grasslands would be lost.
Mr Boyle said: "If you look at the wildlife on the islands, up to 50% of it is reliant upon active crofting. It wouldn't be there otherwise.
"The islands are important to the UK population of corncrakes. About 75% of these birds could be lost if there is a big reduction in the amount of crofting."
The warden said the rare birds and wild plants on the machair had helped boost wildlife tourism on the islands over the last 10 years.
Corncrake are a long-distance migratory species that winter in sub-Saharan Africa and come to the UK in summer to breed.
Their favoured habitat is tall grasses and herbs, particularly hay and silage meadows.
However, in the late 19th Century the mechanisation of farming led to crops being harvested quicker and the corncrake population plummeted. The species became restricted to the Hebridean islands on the west coast of Scotland.
In 1993, the British population was estimated at just 480 males heard calling for mates.
But by the last national survey in 2003 this figure had almost doubled to 832 males.
Since then, annual counts have shown that the population increase continued throughout the 2000s, and in 2007 the population in its Scottish strongholds hit a high of more than 1,270 calling males.
However, this number declined in 2008 by 8% to 1,140.
The Ministry of Defence and contractor QinetiQ plan to make job cuts as part of a proposed £50m in savings.