The US said it launched formal challenges at the World Trade Organization on Monday against China, the EU, Canada, Mexico and Turkey. The partnership between the European Union and Japan is also being strengthened in other areas, the AP reports, such as climate change, defense, and anti-protectionism.
It will cover a third of the global economy and 600 million people, after it is ratified by the European Parliament.
The Japan-EU Free Trade Agreement will eliminate almost all tariffs between the bloc and the world's third biggest economy.
The dialogue will be chaired by Japan's trade and foreign ministers and the European Commission's vice-president for competitiveness, both sides said in a joint statement.
The conclusion of the trade agreement was sped up previous year - putting aside the controversial issue of dispute settlements - as a reaction to Trump's election and first questioning of the global order.
The deal, agreed last December, is "the biggest ever negotiated by the European Union", according to European Commission spokesman Margaritis Schinas.
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Japan and the European Union also agreed on Tuesday to establish a regular dialogue on trade and economic policy, with the first meeting to be held before year's end. Following the signing ceremony, they will seek parliamentary ratification.
The EU will also eliminate about 99 per cent of its tariffs on Japanese goods, including crucially removing levies on Japanese cars from the eighth year after the deal is implemented, and scrapping tariffs on vehicle parts immediately.
Prices of European wine and pork will fall for Japanese consumers, while Japanese machinery parts, tea and fish will become cheaper for Europe.
Japanese auto makers will see an immediate elimination of the up to 4% tariffs now in place for 90% of Japanese vehicle parts - and all tariffs on cars will be eliminated within the next seven years.
Brexit has also weighed on the minds of Tokyo trade negotiators.
Besides the latest deal with the EU, Japan is working on other trade agreements, including a far-reaching trans-Pacific deal. "About 94 percent of the tariffs on European exports to Japan will be lifted, rising to 99 percent in the future".
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But both parties have decided not to include a controversial scheme to settle investment disputes and will continue negotiations over the matter.
It was delayed from earlier this month because Japanese Prime Minister Shinzo Abe cancelled going to Brussels over a disaster in southwestern Japan, caused by extremely heavy rainfall.
In a pointed message, Mr Tusk said: "The real risks to our economy, jobs and prosperity are political uncertainty, tariff war, unpredictability, irresponsibility and aggressive rhetoric".
The digital services sector also looks set to benefit from the European Commission's decision of adequacy in relation to Japan's data protection regime, which paves the way for data transfers between the EU and Japan, including within businesses.
It said: "Tariffs on beef will be cut from 38.5% to 9% over 15 years for a large volume of beef products".
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