The new guidelines apply to the so-called 'non-energy extractive industry' – mining, metals and minerals – whose method of extraction can lead to biodiversity loss.
Areas containing resources such as lithium, magnesium and platinum, which are key in manufacturing day-to-day products such as computers and medicines, can lie in areas covered by the Natura 2000 network of protected ecological sites.
EU Environment Commissioner Janez Potočnik and his colleague Antonio Tajani, in charge of industry and entrepreneurship, said the guidelines will help member states and extractive industries comply with the EU's Habitats and Birds Directives.
"These new guidelines will give member states and industry clarity regarding the undertaking of non–energy extractive activities in accordance with Natura 2000 requirements. There is no change of legislation or policy, but merely guidance on existing law," the two said in a statement.
The mining industry is advised on how to minimise environmental damage by undergoing an "appropriate assessment". As a result, polluting mining projects may still be allowed if measures are taken to minimise their environmental impact.
One of the objectives of the EU's current Environmental Action Programme is to ensure that the consumption of resources "does not exceed the carrying capacity of the environment" and that the linkage between economic growth and resource use is broken.
Critics argue, however, that the move is equivalent to opening up protected sites for mining during the International Year of Biodiversity. "Our central aim is to meet the needs of industry," the commissioners said, "while avoiding adverse effects on wildlife and nature".
EU newcomers such as Poland have struggled to fulfil the Birds and Habitats Directives while being major exploiters of coal and other natural resources. The annual turnover of the EU's non-energy extractive industry for critical resources is €49 billion, employing 287,000 people.
The list of sites covered by the programme has yet to be completed but potentially concerns the 26,000 current Natura sites, most of which are privately owned.
Mining and biodiversity: Friends or foes?
The latest report from the Economics of Ecosystems and Biodiversity (TEEB) project argued that several business sectors have an interest in protecting nature, calculating the annual value of forest loss around the world at $2-5 trillion, for example.
Indeed, the de-watering of mines can add to the presence of heavy metals affecting soil quality and water quality, which are vital to ecosystems and industry alike.
Mining companies have argued, however, that rather than harming the environment, their practice can actually create and preserve new habitats by maintaining shallow pools above mining sites where amphibians can reproduce, for example, instead of refilling exploited pits.
The UN Convention on Biological Diversity will meet in Nagoya, Japan between 18 and 29 October in order to negotiate a post-2010 framework for allowing resource extraction while halting biodiversity loss. The latter was a failed target in the EU's Natura 2000 programme, which ran until 2010.