Total project costs are estimated in excess of 1 trillion yen (US$8.1 billion). Several hurdles remain, however, including finding the funding.
If the project is realized, it would mark the second time Shinkansen technology has been exported. Taiwan introduced the system in 2007.
According to the transport ministry, the rail link will run for about 670 kilometers. However, the actual route, locations of stations and the start and completion dates of the railway construction have yet to be decided.
The two countries said they would undertake detailed surveys to sort out the matter.
They agreed in 2012 to cooperate on building railway infrastructure in Thailand. But this is the first agreement for Shinkansen technology in Thailand.
The Japanese consortium behind the project could comprise East Japan Railway Co.; Mitsui & Co.; Hitachi Ltd.; and Mitsubishi Heavy Industries Ltd.
The Abe administration regards infrastructure exports as one of the pillars of its economic growth strategy. In addition to Thailand, it is holding talks with Malaysia, India and the United States to promote Shinkansen technology.