According to The Guardian, Abe said the deal "shows the world the unshaken political will of Japan and the European Union to lead the world as the champions of free trade at a time when protectionism has spread".
The signing was initially planned to take place in Brussels earlier this month, but Abe canceled a trip due to the rain disaster mainly in western Japan.
Both sides are heralding the deal, which covers a third of the global economy and more than 600 million people. The European Union and Japan are signing a widespread trade deal Tuesday.
European Council President Donald Tusk on Sunday rejected Trump's characterization of the EU as an enemy of the US, saying that the two are "best friends".
The huge deal was signed as President Donald Trump unsettles allies and provokes rivals with his aggressive "America First" trade policy. More than 200 people died from flooding and landslides. But they will bring Japanese consumers lower prices for European wines, pork, handbags and pharmaceuticals. Now signed, the pact requires legislative approval. Japanese machinery parts, tea and fish will get cheaper for Europe.
The pact - which both Japan and the European Union aim to have come into force by early next year - will abolish or reduce tariffs on industrial products and agricultural items between the two sides and sets rules on investment, which is expected to help enhance opportunities for further two-way trade and investment. Eventually, about 99% of tariffs on all imports will be eliminated. The difference reflects exceptions on such products as rice, which enjoys strong political protection from imports in Japan. "The EU and Japan remain open for cooperation", European Council President Donald Tusk, who speaks for the 28 EU national leaders, told reporters.
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Overall, European farmers will benefit, Juncker said, though European consumers will be able to more easily buy luscious Kobe beef and famous Yubari melons.
The major step toward liberalizing trade was discussed in talks since 2013 but is striking in the timing of the signing, as China and the USA are embroiled in trade conflicts.
Trump pulled the United States out of the Trans-Pacific Partnership with Japan and 10 other states on his first day in office in January 2017 and has pushed to renegotiate a free trade pact with Canada and Mexico. The partnership includes Australia, Mexico, Vietnam and other nations, although the USA has withdrawn.
Europe's food sector is one of the biggest winners from the deal, which should allow it to capitalize on Japanese demand for high-quality cheese, chocolates, meats and pasta. Japan's growth remains heavily dependent on exports.
The IMF said in a seperate report: "These measures are likely to move the globe further away from an open, fair and rules-based trade system, with adverse effects for both the U.S. economy and for trading partners".