More than 30,000 Indonesians have fled their homes in the capital due to flooding that has left five dead, officials said Sunday, with people using rubber dinghies and wading through waist-deep water to reach safer ground.

Many parts of Jakarta were under murky, brown water after days of torrential rain produced the city's first significant floods of the months-long rainy season.

Buildings in some parts of the sprawling capital, which has a population of more than 10 million and is regularly afflicted by floods, were half submerged, with roads unpassable in many areas.

"Yesterday the water was knee deep in my house," Yulian Candra, who lives in west Jakarta, told news website Detik. "There has also been a power cut for the past two days."

The number of those forced to leave their homes jumped from less than 5,000 on Saturday to more than 30,000 on Sunday after heavy rain deluged Jakarta overnight.

People waded through the floods clutching their belongings. Others used boats to make their way to evacuation centres, which are mainly housed in mosques in the Muslim-majority country, but also in government buildings and tents erected on the roadside.

Some motorcyclists, cyclists and cars ventured out despite the weather, spraying up water as they drove along roads where the floods were not yet too high.

The flooding was widespread across Jakarta, with the highest number of displaced in the south and west of the city and floodwaters reaching up to three metres (10 feet) in some places.

Five people have so far been killed in the past week due to flooding, disaster agency official Tri Budiarto said, adding that those killed had either died by drowning or being electrocuted.

Flooding is a perennial problem in Jakarta, the political and economic heart of Southeast Asia's biggest economy, a fast-growing, poorly planned city.

"Floods continue to inundate several areas in Jakarta," national disaster agency spokesman Sutopo Purwo Nugroho said. "So far, 30,784 people have been displaced in Jakarta."

Nugroho said there were also flooding in districts surrounding Jakarta, and other parts of Java island.

However he said the floods were yet to reach the same level as last year, which were the worst in five years and saw downtown commercial districts inundated.

More than 50,000 people were forced out of their homes last year, he added.

However Budiarto warned that the number of evacuees may rise in the coming days as more rain was expected.

Meanwhile on northern Sulawesi island, the death toll from flash floods and landslides triggered by torrential rain earlier in the week rose to 19, an official said.

The toll rose when rescuers recovered the body of a woman from a landslide in Tomohon city, local disaster agency chief Christian Laotongan told AFP. He added that around 40,000 people were also still displaced.

"The floods have subsided but houses were wrecked, and furniture and belongings were damaged, so people have not been able to return," he added.

Indonesia is regularly affected by deadly floods and landslides during its wet season. Environmentalists blame logging and a failure to reforest denuded land for exacerbating the floods.