Details of the damage have been shared with resorts and the National Disaster Management Centre.
Moulds were slotted together underwater, like a giant aquatic LEGO set, to create the new reef.
The proposed airport could be unusable because of flood risks.
Most of the trees will be razed for a runway and other airport buildings.
The capital lacks a natural beach and its residents flock to suburb islands at weekends.
Three accidents at sea were reported Saturday morning.
The airport and hotel project would swallow up most of Fainu island.
Greater Malé and nearby local islands generate 774 tons of mixed solid waste daily.
Activists have raised concerns about the need for an airport in Fainu as Raa atoll already has one.
Some 104 million non-biodegradable plastic bags toxic to coral reefs and marine life were imported to the Maldives last year.
Tremors in the central Maldives were the result of reef blasting by a local resort firm.
A swathe of the Kulhudhuffushi mangroves was reclaimed for the airport project last year. The lagoon was reclaimed all the way to the reef’s edge on...
The Met says there will be heavy squally showers and wind speeds of up to 55 miles per hour.
The Met said there would be torrential rain and gusts of up to 45 miles per hour.
A youth group in the Lhaimagu carried out the coral planting programme to revitalise the island's reef ahead of the introduction of local tourism.