Stewart Milne Homes started preparatory work on the site of the former Lochgreen Hospital last month.
But workmen mistakenly moved heavy machinery into the delicate eco-system, a designated local wildlife area, damaging a large part of the site.
Environmental campaigners say the rare heathland may take centuries to recover.
Kieran Sheehan (left) said: ‘‘Lowland heathland is a real rarity in Scotland.’’
The site is home to around 20 grass species as well as orchids and heathers.
Stewart Milne apologised for the mistake and blamed a sub-contractor’s error.