Carrying 102 passengers and 79 crew, the 4,200-tonne liner crashed into the reef at low tide on March 4.
"It will take decades to restore the reef", the lead researcher told the Jakarta Post. They found out that the episode destroyed the marine's habitat especially the eight coral species discovered in the reef, which include the stony Acropora, Porites, Montipora and Stylophora family.
The ship had been grounded despite having Global Positioning System and radar instruments.
Safri Burhanuddin, deputy of human resources science and maritime culture at the Coordinating Ministry for Maritime Affair, said that the evacuation process will have to wait for high tide.
Raja Ampat is a known national park and one of the world's most popular dive sites; therefore, compensation for the damages will cost $800 to $1,200 or an estimated total between $1.28m and $1.92m to be paid by Noble Caledonia. "Was a 12 year old at the wheel?" a horrified owner of a local homestay wrote on Facebook.
'Luxury megayachts pass through quite often.
Although Noble Caledonia ships can be much smaller (the Caledonia Sky sleeps 57) than other tourist ships cruising the seas, it now joins a number of other cruise lines to face criticism after an environmental mishap.
A professional diving instructor, Ruben Sauyai, who relies on the reef for his income, told the BBC he cried when the damage occurred. This is just insane though'.
The vessel set sail from Papua New Guinea Feb. 25 and is scheduled to arrive in Manila next week.
The Indonesian Environment and Forestry Ministry already send their staff in the accident area to assess the damage done to the coral reefs and to collect evidence.
Describing the incident as "unfortunate", a spokesman said "it is imperative that the reasons for it are fully investigated, understood and any lessons learned incorporated in operating procedures".
"The skipper forced the ship to enter the area, which was not open to cruise ships", he said.
The ship has since been refloated and the company said that based on the inspection "the hull was undamaged and remained intact". Numerous attempts to free it using a tug boat failed, and only caused further damage to the corals.
The damage to Raja Ampat, a UNESCO World Heritage Site, drew global outrage. The director of Raja Ampat's tourism agency, Yusdi Lamatenggo, confirmed the accident in the archipelago located at the edge of the Pacific Ocean and the Indian Ocean.