Sixty per cent of Northern Ireland's 54 Special Areas of Conservation are below par, Environment Minister Mark H Durkan has revealed.
His department has now been accused of systemic failure after he admitted it has not carried out any reviews of how minerals permissions are affecting these protected areas since 2000.
The Green Party said the figures proved we were failing our natural heritage, and we face significant fines from the EU if we breach the habitats directive.
The minister (below) revealed that 33 of Northern Ireland's 54 SACs are in "unfavourable condition", in response to an Assembly question by Green Party leader Steven Agnew.
Meanwhile, five sites are in "unfavourable but recovering condition", and just 16 are classed as being in favourable condition.
Special Areas of Conservation (SACs) are strictly protected sites designated under the EC habitats directive as part of a network of habitat types and species that are most in need of conservation at a European level.
In Northern Ireland they harbour rare species such as the marsh saxifrage, the freshwater pearl mussel and Atlantic salmon.
Mr Durkan said: "The department has not undertaken a full review of all extant permissions, but it is undertaking the required review on a case-by-case basis where there are amendments or modifications to applications approved before designation of a SAC, or if it is deemed necessary due to the department becoming aware of a particular issue."
Reasons for unfavourable conditions include a number of factors such as under-grazing and over-grazing by livestock, inappropriate or uncontrolled burning of vegetation, the spread of invasive species, changes in water levels, decline in water quality and atmospheric nitrogen deposition – for example from agricultural sources, road vehicles and industrial sources.
Mr Agnew said it is unacceptable that 60% of SACs are in unfavourable condition, as they are legally protected under European law.
"These figures are certainly very worrying," the Green Party NI leader said.
"The Department of the Environment has not conducted a review of these sites, so it is impossible to monitor whether they have actually improved or degraded.
"SACs are there to protect areas which have special flora or fauna and are supposed to be given enhanced protection under the European habitats directive legislation.
"Again, Green Party NI is calling for an independent environmental protection agency which would monitor important issues like this and ensure our natural environment is managed and protected in an effective way.
"I intend to raise this issue with Environment Minister Durkan."
Questioned by Mr Agnew in the Assembly yesterday, Mr Durkan said there was not a systemic failure, but resources may not have been allocated as they should.
Northern Ireland Environment Agency (NIEA), the natural heritage department within the DoE, is to undergo a restructuring process, as it is important they do their business better and quicker and ensure environmental protection, but not at disproportionate cost to farmers, he said.
He said the DoE was dealing with large numbers of retrospective minerals permissions and he has not determined if a review of how these affect SACs is required.
"The minister has acknowledged that there has been insufficient resources put into the management of Special Areas of Conservation," said Mr Agnew. "However, I disagree with his assessment that there has been no systemic failure.
"I would call on the minister to initiate the required review of minerals permissions. Failure to do so is in breach of the habitats directive and could lead to significant fines from the EU."
The DoE said the condition of features and sites was not expected to improve rapidly as restoration can take time, but the NIEA was working with landowners and other stakeholders to ensure sympathetic management of SACs was in place.