The visit by Zhang Zhijun, the most senior Chinese official ever to visit Taiwan, was a further sign of warming ties between the former bitter rivals despite vocal opposition from Taiwanese suspicious of closer ties with Beijing.
But protests forced Zhang to cancel a visit to a fishing port in southern Kaohsiung city earlier Saturday following clashes between protesters and the police.
One protester splashed a bottle of white paint on his car late Friday.
Zhang, who holds ministerial status, also scrapped two planned engagements in central Taichung city ahead of his departure on Saturday, officials said.
His supporters scuffled with protesters outside a temple in Taichung, with one man sustaining injuries to his head, the Central News Agency said.
Kaohsiung mayor Chen Chu, a senior politician at the China-sceptic opposition Democratic Progressive Party, urged protesters to refrain from violence.
"Taiwanese should be more confident and rationally express their different voices and opinions. We respect any remarks that are expressed peacefully," she told reporters.
She also promised to investigate claims by some protesters that they were mistreated by the police.
Many Taiwanese remain wary of closer relations between Taipei and Beijing. A planned pact to free up the services trade with China sparked an occupation of Taiwan's parliament and mass street protests in March and April.
Opponents have accused the government of trading Taiwan's national interests to Beijing in exchange for marginal economic benefits.
Eight protesters were arrested on Thursday for trying to blockade Zhang while he was visiting a scenic mountain region near Taipei.
On Wednesday, dozens of pro-independence and pro-unification activists clashed at the airport before police separated them. Demonstrators also tried to break through security barriers and clashed with riot police outside a hotel where Zhang was meeting his Taiwanese counterpart Wang Yu-chi.
Zhang and Wang had met in China's eastern city of Nanjing in February in the first government-to-government talks since Taiwan and the mainland split 65 years ago after a civil war.
China considers self-ruled Taiwan as a part of its territory awaiting reunification -- by force if necessary.