The quake affected the Karangasem and Bangli districts on the eastern side of the tourist island and a search has been concluded, the agency said in a statement, but authorities were continuing to monitor situation.
A landslide triggered by the quake killed two of the victims, the agency said. A third was killed by falling debris.
The U.S. Geological Survey (USGS) said the 4.8 magnitude quake struck off Banjar Wangsian, and put its depth at 10 km (6.21 miles).
There were no significant damage in other parts of Bali, while the quake was felt also in the neighbouring island of Lombok, local media reported.
Bali reopened for international tourists on Thursday after 18 months of pandemic restrictions, but they are only expected to start arriving later this month.
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