In order to investigate the dioxin emission levels of hazardous waste incinerators (HWIs), and estimate their emission factors to the atmosphere, flue gas samples were collected from 12 HWIs in China, and analyzed for polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs). Eleven HWIs are located in the south-eastern coastal areas of China, with rotary kilns being is the most widely used type of incinerator (more than 50% of the units), followed by pyrolysis kilns. Eleven incinerators had their emission levels below the current standards in China, while only four facilities exhibited emission levels below the European Union’s limits. The highest concentration of PCDD/Fs, at nearly 1 ng TEQ/Nm3, was in the flue gas collected from an HWI with a waste burning capacity of 5 ton/d. This result was significantly higher than the values found for the other 11 incinerators, and thus was due to the poor performance of air pollution control devices and the influence of memory effects caused by PCDD/Fs emissions related to the start-up of the incinerator. In addition, the high dioxin emissions of this HWI were related to its feeding wastes, which mainly consisted of chemical industry waste residue with high a chlorine content. The emission factors of PCDD/Fs from the HWIs examined in this work were in the range of 0.27–18 µg TEQ/ton hazardous waste, with an average value of 3.74 µg TEQ/ton hazardous waste. It is estimated that 5.0 g TEQ of PCDD/Fs was released from HWIs to the atmosphere in China in 2010, which is less than that seen in 2004. The results of principal component analysis and hierarchical cluster analysis show all the investigated HWIs can be assigned to three groups, as verified by the results of nonparametric statistics. OCDD, 2,3,4,7,8-PeCDF, 1,2,3,4,7,8-HpCDF and OCDF are the main congeners in these three groups.