Damanaki, speaking Thursday at a U.N.-sponsored conference in Paris, called for "decisive action" to "move forward" on a revision of the U.N. Convention on the Law of the Sea -- which governs the high seas beyond national jurisdictions -- to include the protection of marine biodiversity.
Her call came as private companies and scientific teams are stepping up "bioprospecting" in deep-sea areas, seeking sometimes rare marine organisms whose molecular compounds and unique properties can be used in anti-cancer pharmaceuticals, food and other potentially lucrative commercial fields.
That has led to fears of over-harvesting, physical disruptions of fragile ecosystems and pollution in the absence of an updated UNCLOS to protect the diversity of deep-sea marine life.
The European Union, Damanaki said, "is committed to protecting the oceans. Sustainability is a key word here. Oceans can deliver smart, green and sustainable growth.
"We need to make sure that resources are harvested rationally and fairly. We are not there yet. It is now time to take decisive action and move forward."
UNCLOS, since it was established in 1994, has covered only rights to "non-sedentary marine biological resources" such as fish, which belong to whoever catches them on the high seas.
But since then, deep-sea species such as sponges, corals and sea slugs and bacteria collected from hydrothermal vents have become commercially attractive for the enzymes their produce, which can be used in anti-cancer drugs, cosmetics, ethanol production and other products.
"Bioprospecting" marine scientists and companies have identified more than 15,000 molecules, resulting in nearly 700 marine gene patent claims filed by 2009, a Netherlands Institute for the Law of the Sea analysis concluded.
Dozens of products based on deep-sea organisms have been patented, raising questions of how the sea life will be managed.
Damanaki told the Paris conference, which included French Minister of Ecology, Sustainable Development and Energy Delphine Batho and U.N. Educational Scientific and Cultural Organization Director General Irina Bokova -- the European Union is urging a goal of adding a biodiversity protocol to UNCLOS by 2014.
"Today, the number of new products developed from marine species through biotechnology grows by 4 percent every year," she said. "We use these products in the domains of pharmacology, food, cosmetics, agriculture, aquaculture and even biofuel production. We touch upon rare organisms in fragile ecosystems, yet as we are aware, mitigation measures remain uncoordinated.
"A multilateral agreement under (UNCLOS) is clearly needed here. Biodiversity protection has to be an overarching objective of the international community."
Countries attending last year's Rio+20 Conference in Rio de Janeiro committed to agreeing on an updated UNCLOS by the end of the 69th U.N. General Assembly in September 2014.
One of the biggest challenges would be to establish a new entity responsible for administrating access to marine genetic resources and to establish benefit-sharing and monitoring mechanisms.
As part of the effort, UNESCO is proposing the establishment of deep-sea "marine protected areas" and the introduction of environmental impact assessments covering them, which Damanaki said she also supported.