Background: Magnetoencephalography (MEG) has been extensively used to measure small-scale neuronal brain activity. Although it is widely acknowledged as a sensitive tool for deciphering brain activity and source localisation, the accuracy of the MEG system must be critically evaluated. Typically, on-site calibration with the provided phantom (Local phantom) is used. However, this method is still questionable due to the uncertainty that may originate from the phantom itself. Ideally, the validation of MEG data measurements would require cross-site comparability. Method: A simple method of phantom testing was used twice in addition to a measurement taken with a calibrated reference phantom (RefPhantom) obtained from Elekta Oy of Helsinki, Finland. The comparisons of two main aspects were made in terms of the dipole moment (Qpp) and the difference in the dipole distance from the origin (d) after the tests of statistically equal means and variance were confirmed. Result: The result of Qpp measurements for the LocalPhantom and RefPhantom were 978 (SD24) nAm and 988 (SD32) nAm, respectively, and were still optimally within the accepted range of 900 to 1100 nAm. Moreover, the shifted d results for the LocalPhantom and RefPhantom were 1.84 mm (SD 0.53) and 2.14 mm (SD 0.78), respectively, and these values were below the maximum acceptance range of within 5.0 mm of the nominal dipole location. Conclusion: The local phantom seems to outperform the reference phantom as indicated by the small standard error of the former (SE 0.094) compared with the latter (SE 0.138). The result indicated that HUSM MEG system was in excellent working condition in terms of the dipole magnitude and localisation measurements as these values passed the acceptance limits criteria of the phantom test.