Coxiella burnetii causes Q fever, an important zoonotic disease, and exposure is mainly associated with inhalation of contaminated aerosols. In South America, no systematic studies have been carried out. In Chile, the only official record of Q fever has been an outbreak of occupational context occurring in 1998 with eight confirmed human cases, all workers in the Agriculture and Livestock Service. Recently, in 2017 a Q fever outbreak was reported from dairy farm workers in two regions in southern Chile. This study determined the presence of C. burnetii in bulk tank milk samples from dairy farms obtained during this outbreak. A duplex real time quantitative PCR assay with primers and probes targeting two different gene sequences, IS1111 and com1, was used for diagnosis. C. burnetii was detected in 2 of 105 samples analyzed (2.1%). These results pose a potential public health risk as the milk from these farms was sold to the local human population. This is the first report on detecting C. burnetii in raw tank milk samples in Chile.