Filming began on the island on Monday, but heritage chiefs and environmentalists have warned about the impact on the rocky outcrop.
The steep island, which dramatically rises more than 700 feet out of the Atlantic Ocean, is home to puffins, manx shearwaters and storm petrels as well as Guillemots and Kittiwakes.
Film director JJ Abrams and actor Mark Hamill - who played Luke Skywalker in the original trilogy - are among the cast and crew on the set of the latest production, Star Wars: Episode VII.
It is believed shooting on the UNESCO World Heritage Site has been brought forward several weeks, threatening the rare birds which are in the middle of their breeding season.
UNESCO has contacted the Irish Government asking for a report.
Roni Amelan, of UNESCO headquarters in Paris, said they want information on concerns about the preservation of the site and particularly any impact on wildlife.
"We can't speculate what the filming of Star Wars on the site will do to the wildlife," he said.
"We just know that this is going on and we have asked for information."
Stephen Newton, a seabirds expert with Birdwatch Ireland, said he can't get onto the island to check the important colony because of a massive security lockdown, led by the Irish Navy.
This is totally inappropriate in terms of the timing.
Stephen Newton, Birdwatch Ireland
Mr Newton said he was asked by the film producers only days before shooting was to begin if he would help them with an impact assessment to secure permits for filming.
But he refused, arguing it would take several weeks to assess, as many of the species breed underground or in rocky crevices where it would be difficult to see what damage is being done.
"I don't think there was enough assessment on the impact of this, you can't see what is going on," he said.
"The birds could desert the island if they get too stressed out, by the amount of noise and vibration."
The conservationist said the island has been "hijacked" for the shoot which is expected to last several days.
He has demanded Dublin's Heritage Minister Heather Humphreys publish the expert advice she received before signing off on the necessary consents for the use of Skellig Michael.
The Irish Defence Forces confirmed a two-mile exclusion zone has been set up in the waters around the island, which is being patrolled by the 48 million euro LE Samuel Beckett naval ship.
Fishermen and other seafarers have been ordered to stay away from the zone until midnight on Wednesday.
Star Wars: Episode VII is due for release in December 2015.
The latest instalment will see the return of original cast members Harrison Ford as Han Solo and Carrie Fisher as Princess Leia.
Irish actor Domhnall Gleeson, Girls star Adam Driver, Oscar Isaac, Lupita Nyong'o and Andy Serkis also feature in the new film.