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In the 1600s, there was lots of trades between Japan and Taiwan. The Dutch colonised Taiwan as a base for trade with Japan in 1624. During the Kingdom of Tungning era (1662~1683), Japan bought deerskin, sugar and silk from Taiwan and sold Precious metal, porcelain, armors and cotton cloth.Japanese money could be used in Taiwan during that period and Japanese merchants were permitted to live in Keelung.
In 1874, Japanese troops invaded southern Taiwan southern Taiwan to attack aboriginal tribes, in revenge for the killing of 54 Ryukyuan sailors in 1871.
Taiwan was under Japanese rule from 1895 to 1945.
Establishment, early 1950s
After the war between China and Japan, during the occupation of Japan, Prime Minister Shigeru Yoshida (officially the last prime minister under the royal decree by the Japanese emperor), intended to approach the newly established People's Republic of China economically and diplomatically. However, the US rectified this initiative and threatened to boycott the 1951 Treaty of San Francisco if Japan did not to engage with KMT-led Nationalist China (now Taiwan) and the later formation of the Treaty of Taipei (a parallel treaty to the Treaty of San Francisco between Japan and the two Chinas that were excluded). The US required Japan to accept diplomatic relations with the KMT-led Nationalist China otherwise sovereignty to the country would not be restored, effectively maintaining war with the US and keep it under US military occupation.
By taking everything into consideration, in the midst of the US creating its containment policy in Asia, Prime Minister Yoshida shifted his stance with regard to the US administration (to then-US Secretary of State John Foster Dulles), as detailed in the Yoshida Letter, to negotiate a peace treaty with Taipei instead. Also as a result of ratification of the Treaty of San Francisco by the US Congress and Senate, he officially ended Japan's status as an imperial power, officially relinquishing of the island of Taiwan and Pescadores. These actions were drafted into Article 9 of the new liberal democratic Japanese Constitution which dismantled the country's military capabilities to declare war on another country with the reservation of self-defense limitations and later stipulated the Security Treaty Between the United States and Japan, which was also passed and enacted by the majority members of the new Japanese Diet with subsequent security treaties in the post-war era.
With the eruption of Korean War and US and UN intervention into that war, diplomatic relations between the governments of Japan and KMT-led Nationalist China were established following the termination of US occupation of Japan in 1952. Japan led the logistics and artillery production/manufacturing to support the US in the Korean War, which acted as the major stimulus for the revival of the its economy, especially in heavy and light industry, soon evident in the Japanese post-war economic miracle. On April 28, 1952, a formal peace treaty was concluded between the Japan and what is now Taiwan, as the former refrained from recognizing the People's Republic of China at that time. In Article 10 of the Treaty of Taipei (Sino-Japanese Peace Treaty) that retrospects[clarification needed]:
- "for the purposes of the present Treaty, nationals of the Republic of China shall be deemed to include all the inhabitants and former inhabitants of (Taiwan (Formosa)) and Penghu (the Pescadores) and their descendants who are of Chinese nationality in accordance with the laws and regulations which have been or may hereafter be enforced by the Republic of China in Taiwan (Formosa) and Penghu (the Pescadores); and juridical persons of the Republic of China shall be deemed to include all those registered under the laws and regulations which have been or may hereafter be enforced by the Republic of China in Taiwan (Formosa) and Penghu (the Pescadores)."
Bilaterally, Japan had, and still has from members of the Japan Business Federation, strong trading ties with Taipei. Japan played a key financial role in the country's beginnings, giving governmental loans to the Taiwanese government to help with the burgeoning country's economic development on various levels before the Nixon Shock and the severing of ties between the two governments.
Joint Communique, 1972
Regarding the One China Policy, Japan had been an earnest ally to Taiwan, however, global politics pushed Japan to overturn its position. As the attempt to belligerently recover mainland China failed and faded and the Taipei-based government was expelled, voted out of UN in a General Assembly vote, by majority UN member states via United Nations General Assembly Resolution 2758, soon after US President Richard Nixon's visit to People's Republic of China in 1972 and the release of the "Joint Communique of the United States of America and the People's Republic of China," Japan's Liberal Democratic Party-majority government led by Kakuei Tanaka decided to establish formal diplomatic relations with the PRC. Before this, Japan had already had robust non-governmental trading relations with the PRC without formal diplomatic recognition.
As a pre-condition for building ties with the PRC, Japan abrogated and made defunct the Treaty of Taipei in relation to then non-recognized Taiwan polity. According to the "1972 Japan-China Joint Communique", the Japanese government fully understood and respected the position of the government of the People's Republic of China (PRC) that Taiwan was an inalienable territory of the PRC, and it firmly maintained its stand under Article 8 of the Potsdam Proclamation, which stated "The terms of the Cairo Declaration shall be carried out and Japanese sovereignty shall be limited to the islands of Honshū, Hokkaidō, Kyūshū, Shikoku and such minor islands as we determine."
Statements and principles set in the Joint Communique of 1972 were written in the Treaty of Peace and Friendship between Japan and the People's Republic of China in 1978. Japan and the PRC agreed to continue abiding by the treaty when former Prime Minister of Japan Shinzo Abe visited Beijing on 8 October 2006.
Japan-China Joint Declaration, 1998
The 1998, Japan and the PRC signed the Japan-China Joint Declaration on Building a Partnership of Friendship and Cooperation for Peace and Development that stated that Japan was to continue to side with the PRC on the One China Policy, that it "continues to maintain its stand on the Taiwan issue as set forth in the Joint Communique of the Government of Japan and the Government of the People's Republic of China and reiterates its understanding that there is only one China." Japan reiterated it will maintain its exchanges with Taiwan, however in a private and regional forms.
Recent initiatives, 2005-present
In the press conference on 31 January 2006, Deputy Press Secretary Tomohiko Taniguchi announced that, in a speech a year earlier, Minister of Foreign Affairs Tarō Asō had expressed concern regarding peace and stability across the Taiwan Strait on the basis of the 1972 Japan-PRC Joint Communique. The announcement reiterated the Japanese government's position "that we do not take a policy of two Chinas or one China and one Taiwan."
Fishery demarcation, 1996-present
Japan insists, on the basis of United Nations Convention on the Law of the Sea, that Japan is privileged on the fishery demarcation to the southern tip of its surrounding territorial waters, whereas Taiwan asserts that it participates as a fishing entity in the Regional Fisheries Management Organisation on the basis of United Nations Fish Stocks Agreement, such as the admission of IATTC, that also applies on the issue of fishery demarcation with Japan. There were sixteen fishery conferences in total between the two stakeholders, Interchange Association, Japan and Association of East Asian Relations of Taiwan, on fishery demarcation from 1996 to 2009, and the dispute of exclusive economic zone between Japan and Taiwan  is still not resolved pertaining to future negotiations between the two sides. Despite this dispute, the two sides reached a fisheries resource management agreement on April 10, 2013.
On the official international tie between the two governments, think tanks from Taiwan is a member of Asian Development Bank Institute, which is located in Kasumigaseki Building in Chiyoda, Tokyo. 
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