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The official Antara news agency said that, in a separate incident, three refugees were beaten to death by unknown assailants in Ternate in North Maluku province, where thousands of refugees have sought refuge from the fighting in Halmahera.
The agency also said the Indonesian military had confiscated thousands of weapons during a massive sweep in the port city of Ambon - Maluku's provincial capital.
Ambon was reportedly calm but tense as soldiers, police and marines conducted the search. Troops backed by armoured personnel carriers stood guard.
Ambon's military chief, Lieutenant Colonel Arif Mardiyanto, said the sweep would move on to other islands.
He said most of the confiscated weapons were home-made, including daggers, pipe bombs, spears and bows and arrows.
About 1300 people have died in Maluku and North Maluku provinces since sectarian clashes first erupted a year ago.
Last week's death toll in the whole area, estimated at 550, makes it the worst of any religious conflict in Indonesia's 50-year history as an independent nation.
The violence died down only after the army dispatched about 2,000 soldiers on Monday.
The fighting has interrupted normal commerce and some parts of the city face shortages of food and other staples. Shortages of rice and cooking oil have been reported.
The Moluccan islands, to the east of the country, were known as the Spice Islands during Dutch colonial rule.
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