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The US Geological Survey said the quake measured 6.4 and struck at a depth of 8.5 kilometres (5.2 miles) north of Paciran in East Java province.
Two other quakes of lesser magnitudes had struck the same area earlier Friday and were also felt in Surabaya, the nearest city, while buildings in Jakarta, the capital, swayed for several seconds after the third earthquake.
Authorities said a house and a village town hall collapsed in Tuban district.
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Indonesia, a seismically active archipelago of 270 million people, is prone to seismic upheaval because of its location on major geological faults known as the Pacific “Ring of Fire”.
A magnitude 5.6 earthquake last year killed some 600 in West Java’s Cianjur city. It was the deadliest in Indonesia since a 2018 quake and tsunami in Sulawesi killed more than 4,300 people.
In 2004, an extremely powerful Indian Ocean quake set off a tsunami that killed more than 230,000 people in a dozen countries.