The US Geological Survey said the magnitude-6.1 quake occurred at a depth of 10 kilometres and was centred 395 kilometres south of Ambon, the capital of Maluku province.
Indonesia's Meteorology and Geophysics Agency official Tri Handayani said the quake was felt in many parts of the province and some parts of Dili, the capital of neighbouring East Timor country, but there was no danger of a tsunami.
She said that the earthquake did not cause any major damage and there were no immediate reports of injuries.
In 2004, a monster temblor off Aceh shores triggered a tsunami that killed 230,000 people in a dozen countries. Most of the deaths were in Aceh.