China has reacted warmly and although the mainland still claims sovereignty over the self-governed island, both have agreed to set aside thorny political disputes to focus on trade. The two sides signed a pact last month to open up the direct links.
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The flight time is now cut by an hour because the planes are no longer required to fly south through Hong Kong's airspace, a detour Taiwanese authorities had insisted on for security concerns. Cargo ships were required to stop at the Japanese island of Okinawa northeast of Taiwan.
The direct services will save costs and generate new business as both Taiwan and China feel the pinch of the global economic slowdown, said Chiang Pin-kung, head of Taiwan's semiofficial Straits Exchange Foundation.
"This will contribute greatly to our economic development," said Chiang, who signed the air and shipping pacts with his Chinese counterpart, Chen Yunlin.
With annual bilateral trade at about US$100 billion, Taiwanese businesses have pushed for years to end the ban on direct links across the 100-mile (160-kilometer) wide Taiwan Strait.
In Beijing, Xu Lirong, executive vice president of the China Ocean Shipping Group Company, said the direct shipping links will cut the cost of the company's related freight business by 30 percent.
Xinhua News Agency quoted him as saying it would "bring new vigor to economic and trade ties" between the two sides.
Taiwan imposed the ban on regular links six decades ago. Former President Chen attempted to end it but failed to strike a deal with the mainland because of its deep distrust of him.