The quake struck at a depth of 14km kilometres (8.5 miles) under the Alor Sea at about 10:44 (0345 GMT), roughly 77km from the East Timorese capital of Dili, the US Geological Survey said.
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A disaster agency official in Alor, a remote string of islands closest to the epicentre, said the quake was felt strongly in the district for almost two minutes.
"We heard at least one building collapsed," Marthen Daud Ndaumanu Kalabahi told AFP.
"We are still trying to reach remote areas where there is no (phone) connection to see if there is any damage or victims."
Indonesia's national disaster agency spokesperson Sutopo Purwo Nugroho said the quake did not trigger a tsunami but sent people fleeing in Alor.
"Some people panicked and scattered," he said via text message, but added he had heard no reports of casualties or property damage so far.
Indonesia sits on the Pacific "Ring of Fire" where tectonic plates collide, causing frequent seismic and volcanic activity.
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