The PVMBG said the quake was recorded to have taken place at 8:18 a.m. local time on Tuesday, 83 kilometers southwest of Nusa Dua, Bali, at a depth of 65 kilometers.
People gathered outside look at a building, as an undersea quake struck south of Bali, at Barat Daya in Nusa Dua, Bali July 16, 2019.
The United States Geological Survey (USGS), measured the quake at a magnitude 5.7 and said it struck 40 kilometers (25 miles) southeast of Kendalrejo in East Java at a depth of 91.6 kilometers (56 miles).
National disaster agency spokesman Agus Wibowo said two women were killed by collapsing houses and more than 2,000 people have fled to temporary shelters.
The tremor, which was felt as far away as Banyuwangi on the neighbouring island of Java, struck relatively deep at 91 kilometres and no tsunami warning was issued.
In the sparsely populated South Halmahera district, the closest area to the epicentre, around 160 houses collapsed or were damaged when the quake struck.
Another witness said: "I felt the quake for a few seconds, I felt it on the first floor, it felt medium strong".
There was also minor damage at a school, a house and a temple in different areas on the southern side of Bali, according to online portal Balipost.com.
On Sunday, a powerful 7.3-magnitude natural disaster hit the remote Maluku island chain in eastern Indonesia, killing three people and damaging almost 1,000 houses.
People who lived near the ocean left for higher ground despite reassurances from officials that the quake did not have tsunami potential.
On Sunday, a strong quake measuring 7.3 on the Richter scale struck off the Maluku islands in Eastern Indonesia, the USGS said.
Last year, a tsunami hit the city of Palu in Sulawesi, killing thousands.