The death toll previously stood at 43.
The Indonesian province of West Java declared a state of emergency on Friday, as this was an area hit most in the floods with over 30 deaths and more than 170,000 people displaced, according to The Jakarta Post newspaper.
Heavy rains have been pouring in Jakarta and adjacent regions since New Year's Eve.
Public transpiration has been critically disrupted, and several areas got isolated and completely inaccessible for rescuers.