The accident damaged some 13,500 square meters of coral reefs, which could cost over € 15 million, according to Ricardo Tapilatu, an oceanographic researcher at the University of Papua, who led a team that assessed the Damage.
Raja Ampat in eastern Indonesia has always been a top attraction for travellers, home to islands surrounded by a kaleidoscope of coral and fish. A scuba diver's video showed the anchor chain "draped across the entire reef, constantly moving back and forth across the reef and causing a lot of damage as it did that".
The ecosystem's fragile structural habitat has been destroyed, with the loss of coral genera diversity.
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.
An official early evaluation last week estimated the ship had damaged approximately 1,600 sq m of coral in one of the world's most attractive reefs. "Was a 12 year old at the wheel?" a horrified owner of a local homestay wrote on Facebook.
The vessel had set sail from Papau New Guinea on February 25 and was scheduled to arrive in the Phillipines on March 14.
Noble Caledonia, the British-based tour company that operates the Caledonian Sky, said they were "very upset" by the damage, were working to reach a settlement with the government and had set up a fund to help fix the reef. Poerwadi said a team was investigating the full extent of the destruction.
The ship has since been refloated and the company said that based on the inspection "the hull was undamaged and remained intact". If the company disagrees with the settlement, the Indonesian government will take matters to court. "I was born here, I was in tears when I saw this damage", local dive instructor Ruben Sauyai told the BBC.
He believes that given the area's reputation - and the fact that it's a national park - the company should pay $1.28m-$1.92m in compensation.
The Transportation Ministry is determining whether the ship had permission to enter shallow waters and whether the ship was equipped to measure water depth. 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.