But angry protests followed his five-day visit at every turn.
More than 60 police were injured in overnight clashes in Taipei, the National Police Agency said, while local media reported more than 50 protesters and journalists were also hurt.
The ruling Kuomintang and the pro-independence opposition Democratic Progressive Party (DPP), which organised the demonstration, traded barbs over the unexpected violence — the worst protest clashes in 10 years.
DPP parliamentarian Lai Ching-teh claimed the party had abided by their promise of staging a peaceful protest and taken the crowd away from the presidential office plaza on Thursday.
"Those who used violence were sent by the Kuomintang," Lai told reporters.
But the accusation was flatly rejected by the Kuomintang.
"Since DPP chairwoman Tsai Ing-wen led her supporters to the street, she has to take full responsibility for the violence," the KMT said in a statement.
A survey of around 800 people carried out by
On Thursday some 2,200 riot police backed by water cannon were dispatched to
Some threw eggs, rocks, bottled water and petrol bombs at police in an attempt to get past barbed wire barricades.
At a press conference shortly before his departure, Chen, his eyes red, appeared close to tears as he thanked Taiwanese security officials.
"I would like to express our thanks to the police," he told reporters. "They made many sacrifices and shed blood during the tense protests. Words cannot describe our appreciation," Chen said, bowing briefly.
On Thursday, thousands of mainly DPP-supporting demonstrators rallied in central
Organisers put the turnout at more than 100,000 while police estimated the size of the crowd to be 10,000.
The cacophony could be heard for kilometres (miles) around the central government plaza as they moved off, on foot and in vans equipped with loudspeakers, towards the Grand Hotel.
The protesters are opposed to deals that