This is seen as a step to push back the growing sentiment of protectionism and separatism, led by the United States under President Donald Trump.
Japan and the EU launched bilateral negotiations in 2013, but were struggling to achieve breakthroughs in key areas, such as Japan scrapping tariffs on EU cheese and wine and Europe giving greater access for Japanese cars and car parts.
Japan and the EU account for about a third of the global GDP, and analysts say their trade relationship still has room to grow.
