We carried out a calibration of FLOTAC for ciliates Troglodytella abrassarti and Neobalantidium coli based on the selection of a most appropriate flotation solutions, and we also tested its accuracy (i.e., number of detected stages out of known added number of stages to fecal samples) and sensitivity for trophozoites of both ciliates in chimpanzee feces and N. coli cysts in pig feces, compared the detection threshold of FLOTAC with MIF-based sedimentation, and, subsequently, tested the losses of ciliate stages during sample preparation. Nine flotation solutions were evaluated, and ZnSO4 solution (specific gravity [s.g.] 1.2) showed to be the most suitable for trophozoite detection, while Sheather's solution (s.g. 1.33) was selected as most suitable for cysts. The FLOTAC sensitivity in detection of both stages varied: for trophozoites, we found all samples were positive when the intensity of infection 10 trophozoites per gram and higher, whereas for cysts the sensitivity was lower. The accuracy of FLOTAC negatively correlated with infection intensity, and the merthiolate-iodine-formaldehyde sedimentation-based quantification had a lower detection threshold. We demonstrated additional losses of stages of T. abrassarti and N. coli due to their retention in the sediment, which is probably a major reason for discrepancies in the numbers of countable ciliates between both methods. In conclusion, the FLOTAC should not be considered as a gold standard for quantification of intestinal ciliates in primates; instead, we recommend the modified MIF method.