China has never renounced the use of force to take back what it deems a wayward province and has been pressuring Taiwan President Tsai Ing-wen, who leads an independence-leaning ruling party, to concede Taiwan is a part of China.
The United States is Taiwan's only major political ally and sole arms supplier.
"We call on the United States and China, when they improve relations, to not use Taiwan in their own interest or as a chess piece," Catherine Chang, Taiwan's minister in charge of China affairs, the Mainland Affairs Council, told reporters.
Tillerson, Wang in highest-level US-China meet under Trump
Chang urged Beijing to communicate with Taipei "in order to maintain stability and peace in the Asia Pacific region."
The comments come after US Secretary of State Rex Tillerson told Chinese President Xi Jinping on Sunday in Beijing that US President Donald Trump anticipates a meeting "soon."
At issue for Taipei is whether a Trump-Xi meeting will harm Taipei's interests as Washington begins considering a big, new arms package for Taiwan, a move sure to anger China.
"We should seek the greatest advantage in the interaction between the United States and China, to reduce the possibility of Communist China guiding and manipulating the US-China-Taiwan relationship," said Peng Sheng-chu, chief of Taiwan's National Security Bureau.
Peng, who was answering questions at a parliamentary session, didn't elaborate on what steps Taiwan should take, but said that based on the bureau's current intelligence, it was not likely that a new communique that could hurt Taiwan's interests would result from a Trump-Xi meeting.
"But we do not rule out the possibility," Peng said.
Tillerson ends China trip with warm words from President Xi
In December, Taiwan had celebrated a diplomatic coup when Trump, as president-elect, took a congratulatory phone call from Tsai and raised questions about whether he would stick with the four-decade-old "one China" policy.
Trump changed tack last month and agreed to honor the "one China" policy during a phone call with Xi.
Tillerson left China with warm words from Xi on the weekend, ending his first trip to Asia since taking office with an agreement to work together with China on North Korea and putting aside trickier issues.
Xi praised increasing communications in recent weeks between Beijing and Washington, and said he is 'confident' of seeing bilateral relations moving in the "right direction."
Taiwan was discussed during the meeting, but details were not provided.
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