China's top negotiator with Taiwan has signed landmark agreements with his Taiwanese counterpart, in a visit widely seen as helping reduce long-standing tensions between the two sides.

But protests during the visit have shown that large segments of Taiwan's population remain deeply distrustful of the island's long-time rival.

Chen Yunlin, the highest ranking Chinese official to set foot in Taiwan since the two sides split at the end of a civil war in 1949, inked agreements with Taiwan's Chiang Pin-kung that significantly ease transport and trade links.

Under the pacts, the two sides agreed to triple the number of passenger flights and make them daily and direct. Twenty-one Chinese municipalities and cities will offer flights to Taiwan, from the current five.

For the first time, direct cargo flights and shipments will be allowed.

Direct transport links were previously banned due to security concerns. Flights and ships had to detour through third countries or regions, including Hong Kong, Macau, Japan or South Korea.

The new routes will cut flight times from Taipei to Shanghai by nearly two hours and sea navigation times from eight days to four days on some routes - helping both sides save tens of billions of dollars. They are also expected to boost trade and tourism between the two economies, both among the world's largest.

Taiwan is believed to be the main beneficiary of the transport links as they will cut operation expenses for the many Taiwanese businesses with factories and other investments in China.

Semi-official ties

Setting up a mechanism to inform each other of food-safety problems in a timely manner was also among the agreements.

The recent scandal over tainted milk products in China badly affected Taiwan, which imports more from China than from any other country apart from Japan.

At least three Taiwanese children were made ill by milk products contaminated with the toxic chemical, melamine, and panic among consumers hurt local businesses.

Taiwanese President Ma Ying-jeou has made improving his country's long-strained ties with Beijing a priority.

The last time the two sides held talks was in June in Beijing when Mr Chen, the chairman of the Association for Relations Across the Taiwan Straits (ARATS), and Mr Chiang, head of the Straits Exchange Foundation (SEF), signed agreements launching weekend flights and opening Taiwan to as many as 3,000 Chinese tourists per day.

The two semi-official groups handle negotiations in the absence of formal government-to-government bilateral ties.

Prior to those talks, negotiations had been stalled for about a decade.

Mass protests

On the surface, Mr Chen's visit is focused on economic ties, but many people hope that closer trade and transport links could eventually bring about an end to one of the world's most dangerous flashpoints.

"In the past, relations between the two sides were very hostile," says Kou Chien-wen, a professor at Taipei's National Chengchi University. "This visit shows cross-strait relations are headed toward a direction of conciliation."

But at the same time, Mr Chen's presence is also raising concerns about whether the island of 23 million people could lose its sovereignty and self-rule.

The main opposition Democratic Progressive Party (DPP) organised a three-day sit-in to protest against the visit.

On Tuesday night, protesters tried to break through police cordons to enter a hotel where Mr Chen was having dinner with an official from the ruling Kuomintang party. The protest erupted into pushing and shoving, with police armed with shields and batons on the streets near the hotel.

Opposition to Mr Chen's visit and President Ma's pro-China policies is strong among some parts of Taiwan's population, especially those whose ancestors migrated here when emperors still ruled China, and who have little connection to the mainland.

More recent migrants, who fled here along with the governing Kuomintang party when it was ousted by the Chinese Communist Party, and their offspring are more open to the idea of unification. However, few want a democratic Taiwan to unify with a one-party state.

Two weeks before Mr Chen's arrival on Monday, a mass rally against unification in Taipei drew an estimated 600,000 people, according to the DPP.

Earlier in October, Mr Chen's deputy, Zhang Mingqing, was knocked down by a group of pro-independence activists during a private visit to Taiwan.

Security for the Chinese envoy's visit has, as a result, been tight, with 7,000 police deployed on the streets of the capital to ensure order.

Individual protesters, however, have managed to unfurl banners calling Mr Chen a "communist bandit" and telling him to "get out".

One pro-independence group has offered a cash reward to protesters who manage to hit him with eggs.

"The main reason he is here is to use economic means to reach China's goal - unification. It's just like a hook on a fishing line," says Lin Ching-shui, a retired Taipei resident, one of those taking part in the sit-in.

Many young people, who see themselves as Taiwanese rather than Chinese, also participated.

"His coming here is not really good for us. China just wants us to be a part of it," says Hsu Wen-chieh, a 21-year-old college student. "We want the whole world to know we are an independent country."

Beijing wary

President Ma has pledged to safeguard Taiwan's sovereignty and insists the talks will not touch on political issues.

He has also promised to ask China to remove the more than 1,000 missiles targeting Taiwan, but it is unclear the issue will be discussed during Mr Chen's visit.

Beijing still sees the island as part of its territory, and has threatened to take it back by force if Taiwan formally declares independence.

Relations between Beijing and Taipei have improved since Mr Ma came to power, but the strong opposition to the talks indicates he may not have an easy time pursuing policies which include opening the island to Chinese investment and eventually signing a peace accord.

"I'm worried Taiwan will be betrayed by Ma Ying-jeou," Mr Lin said.

Despite such concerns, however, the two sides have agreed to hold regular talks, with the next round of negotiations expected to be held in Beijing next year and to focus on financial co-operation as well as protection for Taiwanese investors in China.