The quake, which registered 6.4 on the Richter scale struck off the coast of Indonesia's West Timor island at around 8.15am (2.15pm local time), the US Geological Survey (USGS) confirmed.
The huge tremor struck at a depth of 5.3 miles in the sea but no tsunami warning has been issued for the area.
Just hours before earthquake a smaller 4.7 magnitude tremor hit the northside of the island.
There are no reports of damage or casualties at this stage.
Earlier this month 436 people were confirmed dead and more than 236 severely injured in a 6.9 magnitude earthquake that rocked the neighbouring Indonesian tourist island of Lombok.
The island is popular with tourists and the series of earthquakes left terrified holidaymakers fleeing the area, as well as many of the picturesque resorts deserted.
The earthquake was around 60 miles southeast of Kupang - capital of the province of East Nusa Tenggara.
At least £263 million ($340 million) in damage was caused by the quakes with more than 350,000 people forced to flee their homes.
Locals in the village of Kokok Putek were forced to conduct Friday prayers in damaged buildings surrounded by rubble in the aftermath of the quake.
Indonesia is a highly seismically active region, and is part of the volatile region on the edge of the pacific known as the Ring of Fire.
The USGS assessment of Indonesia's earthquake risk reads: "The population in this region resides in structures that are vulnerable to earthquake shaking, though resistant structures exist.
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