A health ministry official said 20 people in Jakarta and its suburbs have died as of Sunday afternoon, mostly either by drowning or electrocution.
Rustam Pakaya, a health ministry official, said 339,138 people in Jakarta, Tanggerang and Bekasi had left their homes to seek shelter.
It is a dramatic increase from the 190,000 reported displaced earlier in the day.
Government agencies are struggling to provide aid to the homeless, many of whom are staying with friends or family on higher ground at mosques and government agency buildings.
Some people have attempted to stay in their properties, living on the second floors of their homes and refusing to be relocated by soldiers using rubber dinghies, officials said.
"Fortunately, people here are helping each other," said Yusnizar, a 53-year old living in a housing estate on Jakarta's western outskirts where about 1,000 houses were awash with one-metre high muddy water. Like many Indonesians, Yusnizar goes by a single name.
The floods have also forced the closures of several main roads across Jakarta, while at least two hospitals had to move patients to upper floors.
Many train services were cancelled or delayed.
Power and fresh water supplies were also cut to many areas, adding to the misery of people who opted to stay in their flooded homes.
More than 670,000 people are without electricity.
Indonesia's meteorological agency is forecasting rain for the next two weeks.