CO2 emissions from fossil fuel combustion (FFCO2) are conventionally estimated from fuel used (as activity data (AD)) and CO2 emissions factor. Recent traffic emission changes under the impact of the COVID-19 pandemic have been estimated using emerging non-fuel consumption data, such as human mobility data that tech companies reported as AD, due to the unavailability of timely fuel statistics. The use of such unconventional activity data (UAD) might allow us to provide emission estimates in near-real time; however, the errors and uncertainties associated with such estimates are expected to be larger than those of common FFCO2 inventory estimates, and thus should be provided along with a thorough evaluation/validation of the methodology and the resulting estimates. Here, we show the impact of COVID-19 on traffic CO2 emissions over the first six months of 2020 in Japan. We calculated CO2 monthly emissions using fuel consumption data and assessed the emission changes relative to 2019. Regardless of Japan’s soft approach to COVID-19, traffic emissions significantly declined by 23.8% during the state of emergency in Japan (April– May). We also compared relative emission changes among different estimates available. Our analysis suggests that UAD-based emission estimates during April and May could be biased by -19.6% to 12.6%. We also used traffic count data for examining the performance of UAD as a proxy for traffic and/or CO2 emissions. We found the assumed proportional relationship between traffic changes and CO2 emissions was not enough for estimating emissions with accuracy, and moreover, the traffic-based approach failed to capture emission seasonality. Our study highlighted the challenges and difficulties in repurposing data, especially ones with limited traceability/reproducibility, for modeling human activities and assessing the impact on the environment, and the importance of a thorough error and uncertainty assessment before using these data in policy applications.