The move comes despite mounting criticism from climate activists and some investors over its continued use of power plants that are fired by the dirtiest fossil fuel.
The launch of the 650 megawatt unit, initially slated for February next year, follows the commencement of the No.1 unit with 650 MW output capacity at Yokosuka in June this year.
Both units use an ultra-supercritical (USC) power generation system, the company said. The USC has higher efficiency than older systems in coal-fired plants, making it less polluting.
JERA, a joint venture between Tokyo Electric Power Company Holdings and Chubu Electric Power, said it will continue to steadily replace aging equipment with modern power plants to contribute to stable electricity supply and reduce carbon dioxide emissions.
Japan has built a series of new coal-fired power plants over the past several years as it struggled to restart nuclear power stations, which remain largely offline in the aftermath of the Fukushima disaster in 2011.