The quake measured 6.0 on the Richter Scale, the US Geological Survey has reported.
An earthquake of magnitude 6 is classed as strong, which means it can cause extensive damage to buildings and residential areas.
The quake hit about 250km of Ende on Flores.
It was initially measured at 6.2 but later downgraded by the US Geological Survey (USGS).
The earthquake’s arrival is just days after a calamitous tsunami tore through the country last week on the Sulawesi island.
The USGS has issued no immediate tsunami alerts.
Indonesia is located in the Ring of Fire region, one of the worst affected areas by earthquakes in the world.
It is home to 452 volcanoes, oceanic trenches, volcanic arcs, volcanic belts, and tectonic plate movements.
The area experiences 90 percent of the world’s earthquakes, with 81 percent percent of the largest earthquakes in the world occurring along the Ring of Fire each year.
Indonesian authorities are reportedly scrambling to find survivors and provide shelter, food and water for people who may have been left homeless.
The latest tremors were recorded about 30km (18 miles) south of Sumba between 11.12pm UTC and 12.16am UTC.
The tremors have hit close to Sulawesi, which is still reeling from the catastrophic earthquake than left more than 800 dead.
According to UN estimates, roughly 191,000 people are in urgent need of help after the quake and tsunami wave – which measured up to 6m (20ft).
The earthquake that hit Sulawesi on Friday measured magnitude 7.5.
After the horrific earthquake in Sulawesi, mass burials have begun for the hundreds of victims found so far.
But there are fears there are many more casualties trapped under the rubble and debris from buildings in more remote areas.
Video footage shows a 38-year-old man being rescued from a collapsed buildings in the city of Palu on Monday – three days after the disaster struck.