Although heated tobacco products (HTPs) have become increasingly popular in Japan, little is known about whether these emerging tobacco products are being used within indoor public spaces. Nationally representative data were obtained prior to implementation of a comprehensive smoke-free law in Japan as part of Wave 1 of the International Tobacco Control Japan Survey (February–March 2018). We estimated the weighted prevalence of HTP use within indoor public spaces among tobacco users and compared these to estimates for combustible cigarettes (CCs). Overall, 15.6% of current tobacco users in Japan declared that they used HTPs within indoor public spaces. Any HTP use within indoor public spaces was significantly lower than any CC use (80.1% vs. 96.7%). Dual HTP + CC users reported using CCs more frequently than using HTPs within indoor public spaces (97.7% vs. 76.0%). In conclusion, HTP use is less common than CC use within indoor public spaces. Findings of this study can inform the development of targeted smoke-free policies to benefit public health.