BACKGROUND: Cold and dry conditions were well-documented as a major determinant of influenza seasonality in temperate countries but the association may not be consistent when the climate in temperate areas is closer to that in sub-tropical areas. We hypothesized latitudes may mediate the association between influenza activity and meteorological factors in 45 Japanese prefectures. METHODS: We used the weekly incidence of influenza-like illness of 45 prefectures from 2000 to 2018 as a proxy for influenza activity in Japan, a temperate country lying off the east coast of Asia. A combination of generalized additive model and distributed lag nonlinear model was adopted to investigate the associations between meteorological factors (average temperature, relative humidity, total rainfall, and actual vapour pressure, a proxy for absolute humidity) and the influenza incidence. Kendall's tau b (tau) and Spearman correlation coefficient (rs) between latitude and the adjusted relative risk (ARR) of each meteorological factor were also assessed. RESULTS: A higher vapour pressure was significantly associated with a lower influenza risk but the ARR strongly weakened along with a lower latitude (tau=-0.23, p-value=0.02; rs=-0.33, p-value=0.03). Lower temperature and lower relatively humidity were significantly associated with higher influenza risks in over 65% and around 40% of the prefectures respectively but the strength and significance of the correlations between their ARRs and latitude were weaker than that from vapour pressure. CONCLUSION: Even though the range of latitudes in Japan is small (26 degrees N-43 degrees N), the relationships between meteorological factors and influenza activity were mediated by the latitude. Our study echoed absolute humidity played a more important role in relating influenza risk, but we on the other hand showed its effect on influenza activity could be hampered in a low-latitude temperate region, which have a warmer climate. These findings thus offer a high-resolution characterization of the role of meteorological factors on influenza seasonality.