The tsunami triggered by the Great East Japan Earthquake of March 2011, the strongest quake ever recorded in Japan, deposited tsunami sediments along the coastline of the affected area. Because the sediments contained a wide variety of hazardous chemicals, including organic micropollutants, a method for rapidly evaluating the environmental and human health risks of such chemicals is necessary. For this purpose, we propose a novel three-step scheme designated “rapid screening for environmental micropollutants in emergency situations (REPE)”. In the first step, samples are subjected to target screening analysis using an automated identification and quantification system (TSA-AIQS) involving gas chromatography mass spectrometry (GC-MS). In the second step, the chemicals detected by TSA-AIQS analysis are quantified precisely by conventional target analysis. The third step is risk assessment of the target chemicals. TSA-AIQS analysis of the tsunami sediments detected 63 substances, including polycyclic aromatic hydrocarbons (both native and alkylated PAHs) at high concentrations. These PAHs were precisely quantified by target analysis, and the concentrations were used to assess the health risks posed by oral intake, which were found to be negligible. Our results suggest that the REPE scheme will be useful for rapid, comprehensive screening and risk assessment in emergency situations.