On Thursday, terrified residents ran into the streets as buildings fell in around them when the 6.5-magnitude tremor struck, sparking landslides that buried at least one of the victims.
Among the confirmed dead were three young children, with many people killed by falling debris in and around quake-struck Ambon city.
The region's governor has declared a state of emergency until October 9, the agency said.
Indonesia quake death toll rises to 23: official
"As of Sunday morning, 30 people died and 156 were injured," said national disaster mitigation agency spokesman Agus Wibowo.
On Friday, the agency had revised down the official death toll of 23 to 19 after officials realised some of the deceased has been double-counted.
At least 25,000 people had to flee because their houses were damaged by the strong jolt, Wibowo said previously.
Hundreds of houses, offices, schools and public facilities were also been damaged in the disaster. Authorities have set up emergency tents and public kitchens for the evacuees in several districts.
The United States (US) Geological Survey said the quake struck about 37 kilometres (23 miles) northeast of Ambon in Maluku province at a depth of 29 kilometres.
Indonesia marks one year since deadly quake-tsunami disaster
The Southeast Asian archipelago is one of the most disaster-prone nations on Earth.
It experiences frequent seismic and volcanic activity due to its position on the Pacific "Ring of Fire", where tectonic plates collide.
Last year, a 7.5-magnitude quake and a subsequent tsunami in Palu on Sulawesi island left more than 4,300 people dead or missing.
In 2004, a devastating 9.1-magnitude earthquake struck off the coast of Sumatra and triggered a tsunami that killed 220,000 throughout the region, including around 170,000 in Indonesia.
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