The relationships between cardiorespiratory fitness (CRF) measurements not confounded by adiposity and the prevalence of pre-diabetes mellitus (pre-DM) and diabetes mellitus (DM) are not well known. Thus, we aimed to investigate the associations of visceral fat (VF) and CRF with the prevalence of pre-DM/DM among Japanese adults. The study included 970 individuals (327 women and 643 men) who were 40-87 years old and had complete health examinations, abdominal fat area, and fitness data from WASEDA'S Health Study during 2015-2018. The VF area was measured using magnetic resonance imaging. CRF was measured using a cycle ergometer and was defined as VO2peak divided by fat free mass. The pre-DM/DM was identified based on the questionnaire and fasting blood tests. The odds ratios (ORs) and 95% confidence intervals (CIs) for prevalence of pre-DM/DM were calculated. Seventy-three participants had pre-DM and 48 participants had DM. Compared to the low VF group, the high VF group had a higher prevalence of pre-DM/DM (OR: 1.87, 95% CI: 1.18-2.96), although no significant relationship was observed between CRF and pre-DM/DM prevalence (P for trend = 0.239). The sub-group analyses also revealed no significant relationship between CRF and pre-DM/DM prevalence in the low VF group (P for trend = 0.979), although CRF values were inversely related to the prevalence of pre-DM/DM in the high VF group (P for trend = 0.024). Although CRF was not independently related to the prevalence of pre-DM/DM after adjusting for adiposity, higher VF values were related to a higher prevalence of pre-DM/DM. In addition, CRF levels were inversely associated with the prevalence of pre-DM/DM only among high VF individuals.