To elucidate the linguistic similarity between the alveolo-palatal sibilant [ɕ] and palatal non-sibilant [ç] in Japanese, the aeroacoustic differences between the two consonants were explored via experimentation with participants and analysis using simplified vocal tract models. The real-time magnetic resonance imaging (rtMRI) observations of articulatory movements demonstrated that some speakers use a nearly identical place of articulation for /si/ [ɕi] and /hi/ [çi]. Simplified vocal tract models were then constructed based on the data captured by static MRI, and the model-generated synthetic sounds were compared with speaker data producing [ɕ] and [ç]. Speaker data demonstrated that the amplitude of the broadband noise of [ç] was weaker than that of [ɕ]; the characteristic peak amplitude at approximately 4 kHz was greater in [ç] than in [ɕ], although the mid-sagittal vocal tract profiles were nearly identical for three of ten subjects in the rtMRI observation. These acoustic differences were reproduced by the proposed models, with differences in the width of the coronal plane constriction and the flow rate. The results suggest the need to include constriction width and flow rate as parameters for articulatory phonetic descriptions of speech sounds.