Police did not say who might be responsible for the apparent attack and there was no immediate claim of responsibility.
An angry mob torched local government buildings, shops and homes and set fire to cars and motorbikes in Papua province's Wamena city in a protest by hundreds of people sparked by rumors that a teacher insulted an indigenous student.
A spate of anti-racism protests has reinvigorated calls for political self-determination in West Papua, a region colonised by Indonesia for over half a century.
Indonesia opposes Papuan independence and its military has been accused of ruthlessly eliminating the separatist movement’s leaders in the past. It maintains that the 1969 referendum was binding and legitimate.
The 190-metre vessel, carrying nickel ore, was travelling from Halmahera island to Sulawesi island when it sent a distress call shortly before losing radio contact last week.
Indonesian authorities were hunting for more than 250 inmates who escaped a Papua prison set ablaze during violent riots, as fresh protests broke out in the restive region.
During his trial, prosecutors said Aman Abdurrahman issued instructions from prison that resulted in several terror attacks in Indonesia.
A Surabaya police spokesman said police arrested 13 suspects over the two suicide bombings carried out by two families, after conducting raids in Surabaya and its neighbouring cities of Malang and Pasuruan.
At least 10 people including police officers were injured in the attack, which the police say, was carried out by a family of five including an eight-year-old-child who survived.
The most populous Muslim country in the world, with around 250 million people, has seen escalating religious and ethnic tensions ahead of Jakarta's 2017 gubernatorial election.
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