"It's a natural phenomenon affected by climate change. It's been made worse by negligent behaviour," Masnellyarty Hilman, a deputy environment minister in charge of drafting a national strategy to deal with climate change, told Reuters.

She said warmer seas had heated up monsoon winds that carry moisture from the ocean to the land, leading to extra heavy rain.

"According the meteorology agency, rainfall was at up to 250 milimetres on Thursday and Friday. It was an extreme phenomenon." Flood waters have receded in large parts of Jakarta but many areas remained submerged on Wednesday.

Environment Minister Rachmat Witoelar and green groups have blamed the heavy flooding partly on excessive construction in Jakarta's water catchment areas.

Jakarta has seen a huge construction boom since the Asian financial crisis of the late 1990s, slashing the green areas in the low-lying city that has always been prone to flooding.

Hilman said Indonesia was preparing a strategy to deal with climate change and would submit the draft to the United Nations Framework Convention on Climate Change (UNFCCC) this month.

"We have held inter-departmental meetings and will meet again soon to hammer out final details," she said, adding a drive to reduce greenhouse gas emissions would be part of the strategy.

A United Nations panel said last week that humans were to blame for global warming, and predicted more droughts, heatwaves and a slow rise in sea levels that could continue for more than 1,000 years even if greenhouse gas emissions were capped.

Indonesia could lose 2,000 islands by 2030 because of rising sea levels caused by climate change, Environment Minister Witoelar said last month.

"Indonesia as a tropical archipelago is prone to the effects of climate change, so efforts to mitigate it are critical," said Muhammad Suhud of environmental group WWF.

He said ignorance among officials as well as a lack of money and technology could be a major problem.

"Probably if you talk about climate change to many ministry officials, apart from those from the environment ministry, they will just laugh," he said.