The Indonesian National Board for Disaster Management (BNBP) reported 17 deaths in Bogor, a satellite city of Jakarta, reports Efe news.
According to the BNPB, the rest of the fatalities were registered in Lebak, Bekasi and Tangerang, all satellite cities of the Jakarta metropolitan area, where about 30 million people reside.
Most of the victims died as they were swept away by floodwaters or buried in landslides while others died from electrocution and hypothermia, the government agency added.
The agency said that 182 sites were still flooded, 63 of them in Jakarta, and that many of these areas are still inundated with between 30 and 150 cm of water.
Images posted by BNPB on its social networks showed emergency personnel rescuing residents with the use of lifeguard equipment and pushing small boats through chest-deep water.
President Joko Widodo on Thursday said that priority had to be given to those trapped by the floodwaters.
"The most important thing is to evacuate the victims," Widodo said. "The safety and security of the people must be prioritized. We will work on matters (related to) flood management infrastructure later, after the evacuation is finished."
Some 31,000 people had to evacuate to temporary refuge centres due to flooding caused by heavy rainfall in recent days, which led to several rivers overflowing across the capital.
The floods also affected one of the capital's airports, Halim Perdanakusuma, which resumed normal operation on Thursday after it was forced to close and redirect all its traffic to the Soekarno-Hatta international airport the day before.
The head of the Indonesia's meteorological agency warned Thursday that wet cycles would continue in late January to mid-February.
Floods and landslides affect Indonesia yearly during the rainy season, which peaks between December and February.
( With inputs from IANS )