The National Disaster Mitigation Agency said most of the victims of Thursday's magnitude 6.5 quake in Ambon, the capital of Maluku province
The agency said that at least 117 houses and buildings were damaged and about 15,000 people were being housed in temporary shelters.
Parts of a building at an Islamic university also collapsed in Ambon, the capital of Maluku province.
Local disaster official Albert Simaela said a teacher was killed there when parts of the building fell on her.
The magnitude 6.5 quake was centred 33 km northeast of Ambon at a depth of 18 km, the US Geological Survey said.
Rahmat Triyono, head of Indonesia’s earthquake and tsunami centre, said the inland earthquake did not have the potential to cause a tsunami, but witnesses told television stations that people along coastal areas ran to higher ground in fear one might occur.
Mr Simaela said many people drove to higher ground by motorbike and car, causing traffic congestion in Ambon.
He said a main hospital in Ambon was damaged and patients were evacuated to tents in the hospital’s yard.
“The temblor was so strong, causing us to pour into the streets,” said Musa, an Ambon resident who uses a single name.
He said there were no injuries or damage in his neighbourhood but that people on social media reported damage elsewhere in the city.
The National Disaster Mitigation Agency said the quake caused cracks in a main bridge in Ambon, and pictures released by the agency showed minor damage at Pattimura University in the city.
Several houses, universities and local government offices were also damaged.
With a population of around 1.7 million, Maluku is one of Indonesia’s least populous provinces.
Indonesia, home to more than 260 million people, has frequent seismic activity.
Thursday’s earthquake came two days ahead of the first anniversary of a devastating 7.5 magnitude earthquake in Palu on Sulawesi island.
The disaster claimed more than 4,000 lives, with many of the victims buried when whole neighbourhoods were swallowed in the falling ground.
A powerful Indian Ocean quake and tsunami in 2004 killed 230,000 people in a dozen countries, most of them in Indonesia.
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