The quake shook the tourist hotspot of Bali two weeks after a major quake-tsunami disaster in a central region of the archipelago.
The strong quake was felt in Denpasar on the holiday island of Bali, where panicked people fled from buildings.
The magnitude 6.0 quake hit about 4am Bali time, according to the US Geological Survey.
The accident mitigation agency, shows the damages from an natural disaster in East Java's Sumenep district on October 11, 2018.
Tonny Akbar Mahendro said: "I felt it for about 10 seconds".
Agency spokesman Sutopo Purwo Nugroho said today prayers will be held, collectively, in Balaroa, Petobo and Jono Oge to "end the evacuation of bodies".
An natural disaster Thursday killed three people in Indonesia and rattled hotels where International Monetary Fund delegates are attending a major summit, a fortnight after a quake-tsunami killed more than 2,000 elsewhere in the archipelago.
"The natural disaster happened early Thursday when they were sleeping and the quake suddenly rocked so they didn't have time to evacuate", he said, adding that damage caused by the tremor was not widespread.
Almost 80,000 people were displaced by the disaster, many sheltering in tents outside their destroyed homes. People poured out of their houses.
It struck the island of New Britain this morning, and the Pacific Tsunami Warning Centre said there is now a threat of a tsunami.
"We're not sure what will happen afterwards, so we're trying to work as fast as possible", said rescue worker Ahmad Amin, 29, referring to the deadline, as he took a break in the badly hit Balaroa neighborhood.
"People are traumatized. They don't want to go back" to those places, Nugroho said.
"Are they going to ask our permission before they convert this into a mass graveyard?", he added.
After making a rare appeal for worldwide assistance, Indonesia is now trying to limit foreign involvement in the disaster relief effort. Nugroho said there's no need for worldwide aid other than the four priorities identified by Indonesia.
On Wednesday, Indonesia clarified that its policy on foreign assistance, aid workers and volunteers is "not intended" to prevent them from entering quake-hit Sulawesi. The agency has issued guidelines that say foreign aid workers can be in the field only with Indonesian partners.