Thousands of homes and public facilities in Tenggarong, the seat of Kutai Kartanegara (Kukar) regency in East Kalimantan were inundated on Sunday.
"Let us pray together so that the floods quickly recede in Kukar," Regent Rita Widyasari said.
Kukar administration spokesman, Dafip Haryanto, said the flood was caused by heavy rainfall in the upstream area of Mahakam River that coincided with high tidal waves at sea.
"This caused the water to be retained and flooded the city," he said, adding that the Kukar Disaster Management Agency (BPBD) had handled the situation.
"We recommend people monitor the conditions [as of it may get worse]."
In April, floods inundated 18 villages in the Tabang district, some 10 hours by speedboat from Tenggarong, some areas recorded water levels up to three meters in height.
Water from Mahakam River's upstream area also flooded other low-lying districts such as Kembang Janggut, Kota Bangun, Muara Muntai, Muara Wis, Kenohan, Muara Kaman, Sebulu as well as Tenggarong Kota and Tenggarong Seberang.
Despite of rising water levels, residents remain in their stilt-houses and have prepared wooden planks to escape to the roof.