It was reported that the ship was just finishing up with its bird-watching trip on Waigeo Island when it veered slightly off course, running aground during the low tide and crashing through the coral reefs.
The damaged coral reefs at West Papua's Raja Ampat area is expected to take 10 years to recover.
"The damage caused by boat anchors like this one is already serious enough, but the blockage of a liner in the reefs reaches a level never equaled", said the site.
The vice president demanded that the Caledonian Sky's operator pay compensation as authorities said a criminal act could have been committed and they may seek the extradition of the ship's captain.
Scientists found that the crash resulted in the reduction or loss of diversity of eight coral genera and the destruction of the ecosystem's structural habitat. Now that the reef is badly damaged, locals are anxious that it will greatly impact the appeal of their island to tourists. "They should've waited for high tide".
Stay Raja Ampat, a website that links tourists up with homestays, wrote on its Facebook page: 'How can this happen?
What the coral reef looked like before and after. Was a 12-year-old at the wheel?
The vessel set sail from Papua New Guinea Feb. 25 and is scheduled to arrive in Manila next week.
Mr Victor Nikijuluw, marine programme director at environmental group Conservation International Indonesia, said: "Even when (the reefs) grow back, they will not be as pristine as they were before".
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Noble Caledonia, which operated the cruise ship, considered the accident as "unfortunate" accident.
The ship has since been refloated and the company said that based on the inspection "the hull was undamaged and remained intact".
The Transportation Ministry is determining whether the ship had permission to enter shallow waters and whether the ship was equipped to measure water depth.
Locals were upset and enrage by the damaged done to the corals.
Laura Resti of Raja Ampat's homestay association said what occurred was "counterproductive" for their local tourism aspirations, as coral reefs mainly draw in the crowds visiting the national park.
Raja Amat means Four Kingdoms in Indonesian and sits between the Pacific and Indian oceans.
A petition has since been launched demanding the company not just pay compensation but is present to fix the damage as well.
A 2002 report from Conservation International said it was home to almost 1,400 varieties of fish and 603 species of coral.