More than 500 coconut palms were removed from Lhaimagu island.
The agency tweeted the name and address of three individuals fined for littering.
The protected marine areas are the Kandi-Hera Maakandu channel and the British Loyalty shipwreck.
Tremors in the central Maldives were the result of reef blasting by a local resort firm.
Top Environment Protection Agency officials said they were prevented from warning the housing ministry to stop the ongoing ring road work.
Save Maldives raised concerns about the projects in Maafaru and Funadhoo, saying the Environmental Protection Agency had yet to make its findings public.
The Maldives government is accused of hypocrisy: planning for the destruction of the environment while at the same time championing to save it.
The Environment Protection Agency has fined a Maldivian man MVR111,500 (US$7,200) for capturing and keeping protected birds in his backyard. The hefty fine is the first...
The Environment Protection Agency is assessing the damage caused to the Fuvahmulah reef after a Vietnamese cargo ship ran aground on the southern island's lagoon.
Some 18 massive steel pipes imported for the ongoing construction of the China-Maldives Friendship Bridge are being kept on top of a coral reef near Malé.