The school, which was built in the '70s and has asbestos within its building, was shut at noon and pupils and staff sent home as a precaution so tests could be carried out. Six classrooms, the dining hall and science block were all affected.
The school is expected to remain closed today.
A Highland Council spokesman said workmen had been clearing chips from the flat roof in preparation for the installation of 24 solar panels.
"The vibrations from their work saw ceiling panels come down and cement dust fall to the floor in the classrooms," he said. "There were concerns about asbestos and the decision was taken to shut the school. Sampling and air tests will be held to determine the nature of the dust and a decision will be taken as soon as possible to confirm when the school can re-open."
Two years ago teachers at the school were banned from pinning up posters or notices on certain walls because of concerns the toxic material, which can cause cancer, could be disturbed.
Nairn Councillor Graham Marsden said the closure underlined the need for a new Nairn Academy building because the present school was not fit for purpose.
"In my view it was a sensible thing to do because the last thing we can do is put children at harm," he said. "As far as I'm concerned this adds weight to the argument that really what we need is a new academy.
"The biggest problem with the academy is the building itself. There are a very significant number of people within Nairn who believe it really should be replaced. The view is that there are academies and other school buildings which are way ahead of it and this does bring forward the issue of how appropriate this building is.
"A lot of parents and others agree that it should be replaced, whether that is a realistic view is another matter, but I think it does underline that particular need."
Both Rick Riley and Suzie Clunas of the school's parent council refused to comment on the closure yesterday.