The children spent six months collecting 10,500 vouchers for the potting shed through the Let's Grow scheme by supermarket chain Morrisons.
It was delivered just three weeks ago and a parent helper and staff spent one Saturday assembling the shed.
Pupils had not had a chance to use the shed before its Perspex roof was smashed beyond repair overnight on Tuesday into Wednesday of this week. The culprits also targeted what was left of the greenhouse and it is now completely destroyed.
Primary six teacher Roisin Newell, who is the eco-schools co-ordinator, said the damage was noticed on Wednesday morning and reported to the police.
"It is absolutely devastating. A lot of hard work has gone into this and now we have been left without anywhere to do our planting or potting," she said.
She explained to the Ross-shire Journal the pupils had put a lot of effort into acquiring the shed and building the greenhouse, as part of their ongoing bid to achieve green flag status as an eco-school. The school has already been given a silver award.
Roisin said the children spent six months collecting the vouchers for the shed and they spent one- and-a-half years collecting 1,500 two-litre plastic bottles to build the greenhouse. Canes were pushed through the bottles to make the structure, and volunteers gave up two weekends to build it.
"The children put a lot of time and effort into building it. It took many hours of work," she said.
The greenhouse was first vandalised in the Christmas holidays when the canes were pulled off and crushed.
It suffered further damage during this week's incident when more canes were pulled off and the bottles were strewn over the pitch.
Chief Inspector Mike Coats confirmed that police were investigating the incident which happened overnight when the school grounds were entered and an object was used to smash three panels of Perspex sheeting on an eco-shed.
"Vandalism is a particularly antisocial offence, but this is even worse, given that the eco-shed has been put together by the local kids for all the right reasons," said Ch Insp Coats.
"These children are working hard to build this up into something positive, only to find out it has been mindlessly destroyed for no good reason," he added.
l.bradshaw@rsjournal.co.uk