St Kilda is the remotest part of the British Isles
Unesco is in contact with the UK Government over concerns about the impact a withdrawal of staff from a radar station will have on St Kilda.
Leaving the site on the main island, Hirta, unmanned is part of wider plans to change how military rocket ranges are run.
The National Trust for Scotland (NTS) said the move could affect the islands' dual Unesco World Heritage status.
Unesco said there has been no talk of changing St Kilda's designation.
Its World Heritage Centre told the BBC Scotland news website it was aware of "some issues" concerning the remote archipelago.
A spokesman said Unesco was in contact with the UK authorities to resolve them as part of the normal monitoring of heritage sites.
The World Heritage Committee is meeting in Seville, Spain, from Monday but the spokesman said St Kilda was not due for discussion.
The MoD and contractor QinetiQ plan to control the site on Hirta remotely as part of proposed £50m savings.
NTS said radar personnel were a deterrent against vandalism by visitors and assisted in monitoring potential environmental threats.
A further benefit to NTS is that the military shares travel costs of getting to the archipelago, which lies in the Atlantic, 41 miles from the Western Isles.
The radar station is staffed all year, mostly by civilian staff, while trust wardens stay on Hirta from April to September.
Without the assistance of the MoD and QinetiQ the trust said the islands could lose their status as the UK's only dual heritage site.
The radar station tracks missiles test fired from ranges in the Western Isles.
Plans to cut jobs at the ranges led to angry scenes in the Scottish Parliament on Thursday.
First Minister Alex Salmond accused some Labour MSPs of lacking respect when they barracked islands MSP Alasdair Allan.
The presiding officer called for order when Mr Allan asked for the Scottish Government's response to the cuts during first minister's questions.