Chen, the head of Beijing's quasi-official Association for Relations Across the Taiwan Strait, flew to the island's capital city for the sixth round of talks since 2008.
During a brief welcoming ceremony for him at a hotel in Taipei, Chen hailed the achievements the two former cross-strait rivals had reached during previous rounds of negotiations.
"The Taiwan Strait used to have high waves, but now it has emerged as a major channel between people on the two sides," said Chen.
The first day was marked by sporadic demonstrations organised by radical groups who advocate the island's independence from the mainland and have vowed to follow Chen "every step of the way" during his stay.
TV footage showed that a small group of independence supporters waited for him in the terminal building, as his plane touched down at Taoyuan International Airport outside Taipei.
The moment he stepped out of his limousine, a young pro-independence activist abruptly shouted at him, saying "Taiwan, China, each is an independent country!" The man was immediately taken away by police.
Near Chen's hotel dozens of independence sympathisers chanted slogans against talks between Beijing and Taipei led by President Ma Ying-jeou of the China-friendly Kuomintang party.
"All Ma wants to do is to sell out Taiwan's interest. Therefore any agreements he forges with China will by no means be endorsed by us," said Tsai Ting-kui, the leader of the crowd.
Chen is scheduled to meet his Taiwanese counterpart for talks on Tuesday. Each represents an organisation in charge of exchanges between Beijing and Taipei in the absence of official contact.
"The massive exchanges of visits by the people from the two sides have highlighted the necessity of signing such an agreement," Chen said.
The talks will focus on epidemic-control measures and joint research and development of medicines, herbal medicines and emergency treatment, with Chen expected to return to the mainland on Wednesday.
Ties have improved markedly since Ma came to power in May 2008, with the two sides resuming routine high-level direct talks.AFP