The manuscript presents a methane source characterization in the Tokyo area using mobile measurements of CH₄ and C₂H₆. Although this technique is not novel, this is the first study of its kind in the Tokyo area. It is very interesting to see a comparison with other major cities, where most CH₄ sources are of fossil origin, while in Tokyo biogenic sources seem to be more important. The manuscript is generally well written, and the instrument characterization is well detailed. However, I find the emission quantification method not sound, due to the issues related to the height of the emission release, the distance from the source and different wind conditions, which affect gas dispersion. I am not sure that, given the different meteorological and sampling conditions during the sampling campaigns, it is possible to quantify areal emissions by using the equation yielded during the control release experiment. I see this procedure as a general assessment of emissions rather than a tool for comparing the estimated fluxes to reported emissions, because the level of uncertainty associated with such estimates is simply too high. In the manuscript all these biases are described, but it is hard to reach a conclusion whether emission inventories underestimate methane sources or not, and I would give way less weight to the emission quantification part.

Therefore, I suggest publication after addressing this issue and the following minor points:

 Line 117: the repeatability of..

Line 128: explain here why you chose the 1 ppm threshold. You explained that later, but I feel that we need more explanation at this stage

130: why do the C₂H₆ values by MIRA Ultra vary so much?

137: “The mole fractions here are uncorrected as..”. This sentence is not clear, please rephrase.

Figure 165: change the y axis label. Should this be “difference from the nominal value (ppm)..?”. Please clarify

Line 244-249: I would move these sentences to the result section

Figure 4 (b): could you change the colors of red lines according to the source category (e.g. fossil, biogenic and combustion)?

Line 270-272: Move to the result section

Line 307: I would explain the concept of LP density here

Table 2: I am not very convinced about reporting these emission estimates, see my previous comment

This study provides valuable insights into urban methane emissions in Tokyo, employing mobile vehicle-based measurements of CH₄ and C₂H₆. The work is timely and relevant for improving city-level emission inventories, especially given discrepancies between bottom-up (Tokyo Metropolitan Government, EDGAR) and observation-based estimates. The integration of a controlled release experiment is a strength, although it also highlights significant uncertainties in emission quantification.

The manuscript makes a novel and policy-relevant contribution to understanding urban methane emissions. I recommend minor revisions to address the issues of emission quantification uncertainty, spatial representativeness, and inventory implications. With these improvements, the study will provide a strong addition to the literature on methane emissions in megacities.

Overall, I find this paper suitable for publication after addressing several concerns outlined below.

Minor Comments

L20-24: The abstract’s conclusion is vague. It mentions an inconsistency with local government reports for residential areas but doesn’t specify how. To enhance the impact, clearly state whether the measured emissions were higher or lower than the reported values. This highlights the need for improved accounting in specific sectors and underscores the value of direct-measurement research.

The abstract effectively introduces the scope and importance of the study but lacks quantified uncertainty. Including error ranges (e.g., ± values for emission estimates) or highlighting explicit policy implications would improve clarity for broader audiences.

Line 14-16 The phrase “conversion is not straightforward” is vague. Suggest clarifying what aspects are most uncertain (e.g., dispersion variability, background definition, or calibration transferability).

L64-70: I agree with that “Discrepancy between the local government reporting and the global data commonly used in the atmospheric science community”. The discussion of the discrepancy between local government reporting and global datasets is important and well-motivated. While the year-to-year differences in reported values may not be dramatic, the comparison currently refers to different years (2021 vs. 2023). I recommend explicitly noting this difference in the manuscript, as it will help readers interpret the magnitude of discrepancies more clearly.

L93-95: The study covers ~2,000 km of road network (~10% of Tokyo), with higher coverage in selected wards, particularly near waste facilities. This uneven sampling may affect representativeness and source attribution. A brief note on this limitation and its implications for generalizing results would improve clarity.

L180-220: The Control Release experiment is a valuable addition. However, since it was conducted under specific wind conditions, its generalizability is somewhat limited. It would strengthen the manuscript if the authors briefly acknowledge this limitation and note that further experiments under varied meteorological conditions could be beneficial.

L231-233: The choice of a 0.1 ppm threshold for defining LPs is central but appears somewhat arbitrary. While Tokyo’s relatively low CH₄ enhancements justify a lower threshold, a statistical validation (e.g., false positive/negative analysis) would provide stronger support.

L264-272 and overall results: The use of C2/C1 thresholds (<0.005 biogenic, 0.005–0.1 fossil fuel, >0.1 combustion) is appropriate, but the combustion category is underrepresented (only ~5% of LPs, ~30 samples). Given the small sample size, confidence in combustion attribution is limited.

In dense residential areas with potential mixed sources, interpretation could be more complex. It would be useful to briefly acknowledge this limitation and, if appropriate, mention complementary methods (e.g., isotopes, co-tracers).