A shallow and moderately strong 5.9 quake struck at 2359 GMT, around 40 kilometres (25 miles) off Sumba, an island of some 750,000 people.
It was followed up some 15 minutes later by a stronger 6.0 magnitude quake in the same area at a depth of 30 kilometres.
Sumba lies some 1,600 kilometres to the south of Sulawesi island which was struck by a devastating quake and tsunami on Friday, killing more than 800 people.