Part of Kaimes Special School, in Gracemount, will be closed until Easter after a large section of roof came off during this week’s severe weather.
Concerns were today raised about the impact the disruption will have on the pupils, who find it important to have set routines.
Alasdair Bond, the National Autistic Society’s area manager for Scotland, said: “The recent storms have caused damage and misery and we fully sympathise with what this school is now challenged with.
“Routine is extremely important to those with autism and so they will find the change in location and travel arrangements somewhat unsettling.
“But with the right management and plans in place, their transition should hopefully be a smooth one.”
The school provides primary and secondary education for 96 pupils with additional support needs, most of whom have autism.
Tuesday’s storms also caused “significant” water damage to around two thirds of the secondary school building, prompting education bosses to move 54 pupils in S2 to S5 to the disused Fort Primary, in Leith, while repairs are carried out.
Primary and S1 pupils will continue to attend school in the current building.
Education bosses believe the former Fort Primary, which closed last summer, would offer the “best educational solution” for the decanted pupils while repairs are carried out to their own school.
Work to bring the Leith building back into use has already started, but will not be completed until the end of next week, meaning the decanted pupils will not be able to go back to school until January 16.
New travel arrangements have been put in place to take pupils to the alternative site.
Meanwhile, debris around the playground at the Gracemount site is currently being removed and fencing is under repair.
Sharon Ruderham, who recently organised Edinburgh’s first Autism Gala and has two teenage children with the condition, says some pupils will be more affected by the move to a new school than others.
“Every autistic child is different,” she said. “Yes, they need routine and this could cause trauma for some of them, but for others this might benefit them by getting them to adapt to change.
“Driving the children to Leith beforehand and showing them where they will be going to school will help to lessen any anxiety they might have.”
City education leader Marilyne MacLaren added: “After the severe weather, it is our priority to get children back in school for the start of the term and although this is not going to be possible for pupils at Kaimes, we have acted quickly to ensure there is as little disruption as possible and that the children have a safe environment to work in.
“I understand the difficulties that this can cause, and especially for pupils with additional needs, but we have put plans in place to minimise these difficulties.
“Additional support will be provided if required.”