Flooding is a serious problem in Jakarta, and detailed estimation of flood damage is necessary to design optimal flood management strategies. This study aims to estimate flood damage in a densely populated area in Jakarta by means of a survey, to develop the relationship between flood characteristics and flood damage, and to compare the damage estimates from the survey with the damage estimates obtained by a flood damage model for Jakarta, i.e. the damage scanner model. We collected data on economic losses of the January 2013 flood in a survey of flood-affected households and business units in Pesanggrahan River. The actual flood damage in the survey area is US$ 0.5 million for the residential sector and US$ 0.7 million for the business sector. The flood damage for a similar event in the same area based on the damage scanner model is estimated to be US$ 1.3 million for the residential sector and US$ 9.2 million for the business sector. The flood damage estimates obtained by the survey approach are lower compared to the damage scanner approach due to different ways in obtaining flood damage data and in defining the maximum flood damage per object, the different spatial levels of analysis, and uncertainties in constructing the flood damage curves that were applied in the damage scanner model.