A magnitude-5.8 earthquake struck south-east of Sukabumi city in West Java shortly before 8am local time, the national geophysical agency said.
At 123.7km deep, it shook the capital, Jakarta, where high-rise buildings swayed and people were ordered to evacuate.
Another quake of 4.7 magnitude hit off the West Java coast two hours later, followed by a magnitude 5.3 quake near Sarmi, in Papua province.
A string of earthquakes commonly takes place before a larger quake. Earthquakes commonly hit the country but are rarely felt in Jakarta.
A November 21 earthquake devastated a West Java town and left at least 334 dead in Cianjur district, where buildings crumbled and people treated the wounded in car parks.
The quake left more than 1,000 people injured and was the deadliest since a 2018 quake and tsunami in Sulawesi killed about 4,340 people.
Situated on the Ring of Fire, a region mainly focused around much of the rim of the Pacific Ocean, Indonesia experiences regular earthquakes, volcanic eruptions and tsunamis, making it one of the world's most disaster-prone nations.
Thousands in East Java were evacuated last week after Mount Semeru erupted, forcing entire villages to empty.
About 2,500 people were forced to evacuate, authorities said, with many fleeing the scene on motorcycles.
In Semeru’s last major eruption in December 2021, 51 people were killed when villages were buried in layers of mud.
Agencies contributed to this report