Borneo has the lowest possibility for earthquakes compared to other major Indonesian islands because it is further from active fault lines, the agency said.
Jakarta also deals with frequent flooding because it sits on swamp land.
Researchers believe water supplies may dry out for many in Jakarta and wider Java if Indonesia does not relieve pressure on the megalopolis.
"Jakarta and Java Island are heading towards a clean water crisis, we projected the crisis might happen in 2050," the earth scientist Andreas said, blaming rapid population and industrial growth.