A joint statement signed by nine groups including WWF and Greenpeace said there were "serious gaps in critical areas for their effective protection and the conservation of sensitive habitat types and endangered species: legislation and management, governance, conservation, and necessary resources".
Only 12 of the 174 so-called marine Natura 2000 sites in Greece are governed by a protection regime, and even then, this was "limited to temporary or piecemeal measures".
"In practise, this means that only 3.4 percent of Greek territorial waters are protected (and not fully), at a time when Greece has legally committed itself to the effective protection of at least 30 percent of its marine space by 2030," the statement said.
Though protected marine areas currently cover over 18 percent of Greek seas, their management is "seriously" understaffed and short of funding, the report said.
The environment ministry did not immediately respond when contacted for comment by AFP.
Whilst hosting a global conference on protecting oceans in April, Greece pledged to create two new national parks -- one in the Ionian Sea for sea mammals and turtles, and another in the Aegean for seabirds.
At the time, ecology groups noted that the Ionian Sea park is to be created in an area already earmarked by Greece for hydrocarbon exploration.
Greece has been repeatedly fined by the European Commission over environmental issues in the past decades.
In December, it was referred to the EU Court of Justice for failing to implement maritime spatial planning guidelines.
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