Nature Trust had condemned the dumping of debris on garigue in Comino, for illegal road works.
Referring to a report carried earlier this week on Times of Malta, the NGO called on Mepa to identify the culprits and make them pay.
"Unfortunately many working committees even those set up by Mepa over the years have not been able to help the conservation of this Island despite its ecological importance," the NGO said.
"A sense of abandonment can be noticed not only on the garigue but also on other areas such as boats and sun beds out of control at Blue Lagoon, dumping of rubble and waste all over the Island and uncontrolled activities at San Marija Bay."
Comino is one of the 39 designated Natura 2000 sites for the Maltese Islands.