"The government is committed to protecting and preserving the Maldives’ exceptional biodiversity," environmental minister Mohamed Aslam said.
"The marine environment is the bedrock of our economy, supporting our largest industries, tourism and fisheries.
"Not only will this initiative protect whale sharks, but also other mega-fauna including manta rays and reef sharks."
In March, Maldives imposed a country wide ban on reef shark hunting.
Whale sharks grow to 12 meters in length. Maldives says it is home to the only known aggregating population in the Indian Ocean. They are filter feeders and largely survive on plankton.