Nearly 70 percent of the mangrove has been reclaimed, NGOs said.
The death toll from floods in Kerala state rose to 79 by Thursday afternoon, the Times of India reported.
Details of the damage have been shared with resorts and the National Disaster Management Centre.
Neither the Housing Ministry nor the island council has contacted families about relocation plans.
An airport and hotel project would swallow up most of Fainu island.
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.