However, for tens of thousands still in cramped and sometimes unsanitary temporary shelters, the wait to return home could be lengthy.
In one South Jakarta neighbourhood about 30 policemen worked with residents on Sunday to clean up mud one to two metres deep left inside their houses by the floods, which began with torrential rains more than a week ago.
Some people faced worse problems. In the suburban area of Tangerang, water was still two-metres deep in some places and had turned black, causing skin diseases and diarrhoea, Yus, the chief of the neighbourhood unit, told Elshinta news radio.
He added that officials lacked boats to get stranded people to safer areas, although some residents had made rafts from scrap material.
Estimates of deaths from the floods vary. The national disaster co-ordination agency put the figure at 48 on Sunday for Jakarta alone, while one newspaper said another 32 people had died in West Java and Banten, which would make the total 80.
Fears lingered that disease could spread as people stay in emergency shelters or move back into houses often lacking clean water and working plumbing and power.
The authorities are on guard for diarrhoea, cholera and skin diseases, among other illnesses.
The rainy season has several weeks left to run.