Work on the 200-pupil Brynna county primary should have been finished before the beginning of term.
Instead, the school has suffered nearly Pounds 100,000 worth of damage, and is closed for the foreseeable future.
Thirty reception pupils have been forced to begin school life in the local methodist chapel. Five teachers and the rest of the children are being bussed to nearby Dolau primary where huts have been hastily erected in the car park and playground.
Head Pam Mahoney says: "I'm a bit like the flying doctor at the moment. I'm commuting between Dolau, the chapel and my temporary office in an undamaged classroom in the proper school. We were very worried how the children would cope, but they seem to be treating it as a big adventure."
Brynna primary, a typical turn-of-the-century brick structure in an old mining village, was to have an extension, extra classrooms and a new roof as part of a Pounds 500,000 modernisation programme.
Phase one scheduled to be carried out over the summer holiday involved putting on the roof and the construction of internal walls to create new rooms.
Kim Ryley, director of education for Rhondda Cynon Taff council, said: "Three days before term began we had a bit of a sixth sense that all might not be right and decided to go down and check.
"It was an unbelievable sight. There were great piles of rubble and puddles of water everywhere. Halfway through the roof replacement they'd packed up for the August bank holiday weekend and left it uncovered.
"Unfortunately there was a three-day storm. It would be fair to say there was as much water in the school as there was outside."
The rain had flooded through the building, causing thousands of pounds worth of damage.
Mr Ryley says: "Staff had spent ages carefully packing and storing everything before the holidays. Unfortunately the builders chose to move the boxes into the hallway, directly beneath the gaping hole in the roof."
Books, PE kit, curriculum materials and pupil work were all ruined.
Mr Ryley says the staff are devastated: "Anyone who works in the teaching profession can understand the emotional attachment to teaching plans and pupils' work. Equipment can be replaced but the hours of work that went into building an individual teacher's own resources can't be."
The contractors are the council's own building section and the site manager has been suspended pending an internal investigation.
In a letter to the governors, Ms Mahoney said she is appalled that "a school so cherished and respected has been so violated and desecrated. That may sound a bit strong, but you have to understand that this is such a small community, most parents are old pupils."
Staff were hoping to be able to resume teaching at the school by half-term, but the council's property services department estimate it will not be ready before Christmas.