The deal was struck at the fifth Myanmar-Thailand Joint High-Level Committee Meeting that was attended by top officials from all three countries.
Japan's equity holding will be equal to Myanmar's and Thailand's.
The SPV currently has maximum registered capital of Bt100 million.
Thai Deputy Prime Minister Somkid Jatusripitak said the Myanmar government had given top priority to the Dawei project since it would not only help Myanmar's economic expansion but also contribute to the prosperity of many other countries in the region, including Thailand.
Thailand is currently developing land-transport connectivity along the East-West Economic Corridors linking the country's Eastern Seaboard with the Dawei deep-sea port and industrial estates.
Previously, Myanmar was not sure if Japan would join the Dawei SEZ, so initial projects were small, such as a two-lane road, a power plant and an industrial park.