Last week, a judge said the department had not carried out a proper Habitats Directive assessment.
He said the executive had to be on the right side of the habitats directive.
Environment tries to ensure everyone follows the rules of the EU Habitats Directive and protects the environment.
Regional Development minister, Danny Kennedy, said his department "will now prepare the necessary submissions in relation to the Habitats Directive".
Mr Justice Stephens said the Department of Regional Development should have carried out a Habitats Directive assessment but had not done so.
Cornwall gave its final approval to the project in November, but opponents hope to use the EU Habitats Directive to stop the project.
The committee's motion called on the executive to introduce measures to protect and restore the modiolus habitat in line with the EU's habitats directive.
That is what could be on the cards in a few weeks time following a complaint to Europe over an alleged breach of the EU Habitats Directive.
Mr Justice Stephens found that there had been a failure to carry out an appropriate assessment of the rivers Foyle and Finn special areas of conservation under the Habitats Directive.
PlymWIN claimed the planning permission breached the EU Habitats Directive because it did not carry out the appropriate assessment for a project that could significantly affect a European site of importance.
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Chris Howe, head of future landscape for the World Wildlife Fund (WWF), says the group has been campaigning for stricter application of the Habitats Directive for all member states, since its introduction in 1992.
The judge had previously said he was minded to quash the decision to proceed with the project because, he said, the department had failed to carry out an appropriate assessment of the rivers Foyle and Finn special areas of conservation under the Habitats Directive.
The problem has long been recognized, and the aforementioned Habitats Directive -- a corollary of the 1979 Bern Convention on the Conservation of European Wildlife and Natural Habitats -- introduced a range of measures aimed at protecting endangered species (including plants, birds and fish as well as mammals).
She was angry that MEPs turned down an opportunity to oblige farmers to earn subsidy by obeying the existing Water Framework Directive and Birds and Habitats Directives.
The directive protects animals and plant species, and their habitats, considered to be of European importance.
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