Following the first attempt at producing gas from a naturally occurring methane hydrate (MH) deposit in the Daini–Atsumi Knoll in the eastern Nankai Trough area off Honshu Island, Japan in 2013, a second attempt was made in April to June of 2017 at a nearby location using two producer wells sequentially and applying the depressurization method. The operation in the first borehole (AT1-P3) continued for 12 days with a stable drawdown of around 7.5 MPa and 41 000 m³ of methane gas being produced despite intermittent sand-production events. The operation of the other borehole (AT1-P2) followed, with a total of 24 days of flow and 222 500 m³ of methane gas being produced without sand problems. However, the degree of drawdown was limited to 5 MPa because of a higher water production rate than expected in the second hole. The pressure and temperature sensors deployed in the two producers, along with the two monitoring holes drilled nearby, gathered reservoir response data and information about the long-term MH dissociation processes in the vicinity of the production holes in the temporal and spatial domains. Although the ratio of energy return to the input was considerably larger than that for the depressurization operation, some observations (e.g., the high contrast in the production rates between the two holes and the almost constant or slightly reduced gas production rates) were not predicted by the numerical models. This failure in prediction raises questions about the veracity of the reservoir characteristics modeled in the numerical simulations. This paper presents the operation summaries and data obtained with thought-experiment based-anticipated production behaviors and preliminary analysis of the obtained data as the comparison with expected behaviors. Detailed observations of gas and water production, as well as the pressure and temperature data recorded during the gas flow tests, indicate that the heterogeneous MH distribution within the reservoir was mainly responsible for the discrepancies observed between the anticipated and actual behaviors. Furthermore, the motion of the water that does not originate from MH dissociation introduces complexity, such as the occurrence of concentrated water-producing intervals and unexpected gas production responses to decreases in pressure, into the production behavior. The influence of heterogeneity should be clearly understood for the accurate prediction of gas production behavior based on MH reservoirs.