New legislation gives full protection to the creatures across all the waters surrounding Southeast Asia's biggest country, which for years has been the world's largest shark and ray fishery.
Protection group Conservation International hailed the "bold" move and said it was influenced by a recent government-backed review that showed a single manta ray was worth one million dollars in tourism revenue over its lifetime.
This compares to between USD 40 and USD 500 if caught and killed, the group said.
The gentle beasts have wingspans up to 25 feet (7.5 metres), which they flap to propel themselves gracefully through the water.
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"Indonesia now has the second-largest manta ray tourism industry in the world, with an estimated annual turnover of USD 15 million," said Agus Dermawan, a senior official from the ministry of marine affairs and fisheries.
"Given the huge area of reefs and islands in our country, if managed properly, Indonesia could become the top manta tourism destination on the planet."
Taking tourists out to view rays and other creatures provides livelihoods for many people working in popular dive spots across Indonesia, such as Raja Ampat off the northwest tip of New Guinea island and around the resort island of Bali.
In recent years their numbers of rays have declined rapidly, however, due to voracious demand in China for their body parts for use in traditional medicine.
The new legislation protects manta rays within Indonesia's 5.8 million square kilometres of ocean, banning fishing of the rays and their export.
The International Union for Conservation of Nature classifies both species of manta ray as vulnerable.