A group of youngsters, wrapped in iron chains and ropes, occupied a road in an attempt to stop the car of Zhang Zhijun, the most senior Chinese official ever to visit the island, the Liberty Times newspaper reported.
The youths were taken away by police for questioning before Zhang's car approached, the report added.
Zhang, director of China's Taiwan Affairs Office, is on a four day visit to the island in a further sign of warming ties between the once bitter rivals, despite vocal opposition from many Taiwanese suspicious of closer ties with Beijing.
Television footage also showed two protesters being removed by police at a separate location in Wulai after they shouted "Zhang Zhijun get out" and "Taiwan, China, each side is a country" while the senior Chinese official was nearby.
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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.
Yesterday, 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.