For optimum activity of daptomycin (DAP) in vitro, medium supplemented with calcium ions at physiological concentration (i.e., 50 mg/l) is required for determination of DAP minimum inhibitory concentration (MIC) in the Clinical and Laboratory Standards Institute (CLSI) broth microdilution (BMD) method. However, our literature review found that Mueller-Hinton agar (MHA) brands used for the DAP Etest had different calcium ion (Ca²⁺) concentrations among the reports. For 98 clinical methicillin-resistant Staphylococcus aureus isolates previously unexposed to DAP, MICs were assessed by use of the Etest with MHA plates with different media (MHA-A, MHA-B, and MHA-C) and compared with those from the CLSI reference BMD method. The instructions for the Etest recommend MHA with Ca²⁺ of 25-40 mg/l for DAP MIC testing; Ca²⁺ concentrations for each type of MHA were 20.4 mg/l in MHA-A, 45.2 mg/l in MHA-B, and 52.0 mg/l in MHA-C. When the MIC₅₀/MIC₉₀ of the clinical isolates were studied, the Etest MICs for MHA-A were 1-fold dilution higher than for the BMD value. In contrast, for MHA-B they were 1-fold dilution lower, and for MHA-C MIC₅₀ was 1.5-fold dilution lower and MIC₉₀ was 2-fold dilution lower. MICs measured in MHA with higher Ca²⁺ tended to be lower. Comparison of MICs between BMD and the Etest for each MHA showed they were significantly different (p < 0.0001). The correlation coefficient was 0.6258 (p < 0.0001) for MHA-A, 0.4224 (p < 0.0001) for MHA-B, and 0.2504 (p = 0.0129) for MHA-C. Our results suggest there are differences in DAP MICs between MIC testing methods and differences between Ca²⁺ concentrations in MHA. For more objective and accurate measurement of DAP MICs, there should be discussion about standardization of Ca²⁺ in MHA.