"This is just the beginning," he told the Associated Press news agency, adding that houses up to 1.6km inland could be affected.
"It's getting worse and worse."
Rising sea waters pose a threat to coastal cities like Jakarta, which has sunk at least two metres in the last three decades due to factors such as excessive ground water extraction, experts say.
Hahm said that the government should build a dyke to protect Jakarta Bay but conceded that it "will cost billions of US dollars".
Flooding in the Indonesian capital in November last year saw thousands of homes submerged to roof level.
The 18 year high tide cycle occurs when the sun and moon are in direct alignment and making their closest approach to the Earth.
Experts say that Indonesia, one of the world's largest contributors of carbon dioxide emissions caused by rapid deforestation, is also at risk of becoming one of the biggest victims of climate change.