This study aims to provide a quantitative overview of the energy policy regulations concerning the Japan spot market liberalization and analyzes the market clearing price (MCP) and the regional spot prices based on the hourly contribution of the supply stack mix and the merit order effect. In addition, it estimates the regional spot prices interdependency on the MCP. The study acquires an hourly dataset in panel data format from 2016 to 2020 with total observations of 438,240 data records. The developed econometric models include panel data regression using fixed-effect estimator, ordinary least square, and two-stage least square equations. From the results, a one GWh addition from nuclear, hydroelectric, geothermal, biomass, solar, or wind power production technologies decreases spot prices. Contrarily, adding one GWh from thermal, hydroelectric storage, or regional interconnections raises the spot prices by 27.4, 606, 103 ¥/MWh, respectively. The spot prices of Hokuriku and Chugoku tend to offset the price spikes in Kansai, while Tokyo and Tohoku spot prices are significantly related. Adding one ¥/kWh to Tohoku spot price is estimated to raise the MCP by 0.35 ¥/kWh, while the addition of one ¥/kWh to Tokyo spot price is estimated to increase the MCP by 0.04 ¥/kWh. Furthermore, Kyushu and Tohoku, followed by Chubu, have appreciable control over the MCP. The study further highlighted policy implications to constrain the applications of hydroelectric storage as the costliest solution to balance the intermittency of renewable energy sources.