Sha Hailin, a standing committee member of the Communist Party in the city and head of the United Front Work Department there, is the highest-level mainlander to visit since cross-strait ties worsened under Taiwan's new government.
He arrived in Taipei for an annual forum on municipal exchanges as protesters shouted "Sha, go back to China!" at the capital's Songshan airport.
Dozens of demonstrators waved placards reading "Expel propaganda communist, defend Taiwan's sovereignty" and "(Taipei mayor) Ko Wen-je sells out Taiwan". Some supporters also rallied outside the airport with welcome signs.
Sha, who heads the visiting delegation in place of Shanghai Mayor Yang Xiong, made no comment to reporters but waved to supporters.
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Relations with China have grown increasing frosty since Tsai Ing-wen of the Democratic Progressive Party won the presidency in January. Beijing is highly suspicious of Tsai because her party is traditionally pro-independence, and has warned her against any attempt at a breakaway.
Taiwan has been self-ruling since splitting with the mainland in 1949 following a civil war but has never formally declared independence. Beijing still sees it as part of its territory awaiting reunification, by force if necessary.
Critics claim Sha, as Shanghai's propoganda chief, intends to push during his visit for reunification and accuse Taipei mayor Ko of "selling out" to Beijing.
"We are very angry and we refuse China's propoganda to reunify Taiwan. Taiwan is an independent country. We must maintain our sovereignty and dignity," said protester Sherry Huang from the pro-independence Taiwan Solidarity Union (TSU) party.
The TSU said it planned another demonstration tonight at a welcome dinner for the Shanghai delegation in Taipei city hall, and vowed to protest throughout Sha's stay.
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