The three deaths in East Java occurred after buildings collapsed while people were sleeping, an official said.
At least three people were killed as a shallow 6.0-magnitude earthquake struck off the coast of Indonesia's Java and Bali islands Thursday, a government official said.
The victims in East Java's Sumenep district perished after being crushed by collapsed buildings, national disaster agency spokesman Sutopo Purwo Nugroho said.
"The earthquake 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.
The strong quake was felt in Denpasar on the holiday island of Bali, where panicked people fled from buildings.
"Wow, that was really strong and it lasted a long time," said a woman named Davy who took refuge in the parking lot of a Bali hotel, several kilometres from where the IMF and World Bank are holding their annual meetings this week.
Some guests at the hotel in Nusa Dua, south of Bali's main international airport, briefly fled outside after the strong tremor shook the building.
"The quake was very big. I immediately woke up and took my little kids out of the house," Ni Komang Sudiani said.
"All my neighbours were also running," said the mother of two.
The tremor's epicentre was in the Bali Sea around 40 kilometres (25 miles) off the eastern end of Java island, according to the United States Geological Survey.
The quake was also felt in Surabaya, the capital of East Java province, which is about 200 kilometres from Situbondo, the nearest town to the quake epicentre.
"I felt it for about 10 seconds. People were sleeping but got woken up by it," Tonny Akbar Mahendro said.
No tsunami warning was issued for the earthquake.
"The quake didn't trigger any tsunami for sure," Dwikorita Karnawati, head of Indonesia's geophysics agency, said.
The tremor comes after a 7.5-magnitude quake and subsequent tsunami struck off the Indonesian island of Sulawesi – around 1,000 kilometres northeast of Situbondo – last month, killing more than 2,000 people.