Dunvegan Primary School is the latest building to fall victim to the severe rain.
The school's disused basement became severely flooded with groundwater.
A local maintenance team is arranging for the water to be pumped out of the area, which will then be dried out.
Elgar Finlay, Chairman of the Dunvegan Primary Parent Council, described the crisis as an "emergency situation" today (Tuesday 9 October.) He shared a video of water pouring through the walls of the basement and noted that this was directly below the children's classroom.
Mr Finlay stated: "It is only a matter of time before this school causes serious health issues for our children.
"I have no idea if the structure of these walls remains safe or if the school could collapse."
Mr Finlay continued: "The need for a new school for the area was recently highlighted to have been ongoing for over 30 years and having been removed from the Highland Councils capital plan due to budget cuts, having previously been told we were getting a new school is causing further distress and damaging our community. The conditions of the school are now simply unsafe, for educational purposes they are appalling and have been for some time. Our community is rightly becoming more angry, each week that passes as there is another significant issue being reported.
"The school has no security (tourists have walked in to classrooms) this has been reported since 2014, we have a road running through the playground, we have children having to cross a zebra crossing to reach another building just to use the toilet, there are holes in the walls of our classrooms, our nursery door needs replaced but there is no budget available for a new door. Within two weeks of opening for the new 2018 school year the canteen was closed due to burst pipes."
Kate Forbes MSP said: “This is an exceedingly concerning situation that must be resolved as a matter of urgency. It is the latest evidence that parents and pupils deserve a brand new school.
“I will raise the matter with Highland Council, as they are responsible for the school estate. Dunvegan Primary needs to be on the Highland Council’s list of priority schools for the sake of the children."
Highland Council stated: "Arrangements will be made to permanently fill in the disused basement area. Pupils have not been affected and a dehumidifier has been placed in the classroom as a precaution.
"Dunvegan was listed as one of the Council’s priorities for bidding to Scottish Government for funding. We still await an announcement from Scottish Government about future schools capital funding. The Council has progressed discussions with the community, and developed and discussed outline plans with them so the Council can be in a position to make a positive funding bid when the opportunity arises.
"In the interim, pupil safety is a priority and any essential health and safety works will of course be addressed."
Chair of the Care and Learning and Housing Committee, Councillor Andrew Baxter said: "We've put a very strong case to the Scottish Government as to why the Highlands should be treated differently when it comes to funding for our schools. This is because of our high number of small schools, many in remote areas, that cost the council much more to maintain compared to elsewhere in Scotland.
"The problems faced by pupils, staff and parents in Dunvegan demonstrates why we need additional support."