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Discussions on service trade agreement will focus on cutting and removing restrictive measures gradually, enlarging the service sectors covered, and enhancing cross-Strait cooperation.
Meanwhile, discussions concerning cross-Strait investment aim to establish an investment protection mechanism, enhance transparency of relevant regulations, reduce restrictions on investment, and facilitate unhindered investment.
They would also help promote cooperation between small and medium-sized enterprises across the Taiwan Strait, and help economic and trade organizations to set up offices on each other's side of the Strait.
In addition, the mainland and Taiwan will jointly set up a committee for cross-Strait economic cooperation to ensure ECFA agreements can be reached and to supervise the implementation of the ECFA.
The committee will also interpret terms of the ECFA and publicize major information concerning cross-Strait economics and trade.
The committee will hold routine meetings every six months and may have interim meetings upon agreement by the two sides.
The committee will also serve as the authority to deal with ECFA-related disputes until the two sides reach a separate agreement on dispute settlement.
Negotiation for the dispute settlement agreement will start within six months of the ECFA taking effect.
Also on Tuesday, a separate agreement on intellectual property rights protection (IPR) was signed by the ARATS and the SEF.
According to the IPR agreement, the Chinese mainland and Taiwan will increase exchange and cooperation to boost protection of patents, trademarks, copyright and plant variety rights (PVR).
After the SEF and the ARATS achieved the two agreements, scholars from both sides of the Strait expressed a positive view on the future development of the cross-Strait relationship.
"Service trade directly benefits common residents living on both sides", said Andy Chang, professor in the graduate institute of China studies at Taiwan-based Tamkang University.
Also, high-quality service industries would provide more choices for the mainland population and the ECFA will also promote cross-Strait investments from manufacturing industries to the high value-added service industries, Chang said.
Further, the ECFA would not only be a mutually beneficial platform for the mainland and Taiwan, but also a channel for both sides to better connect to other economies in the Asia-Pacific region, he added.
Although profits from some industries on both sides will be affected, many more industries will benefit, said Guo Li, associate professor with Huaqiao University based in southeast Fujian Province.
The ECFA will also provide an opportunity for those affected industries to speed up their industrial upgrading and find new market orientations, which will also help Taiwan improve its industrial structure, Guo said.
Some mainland and Taiwan businesspeople interviewed by Xinhua said they were happy about the signing of the ECFA since they saw "tangible" benefits and profits from the agreement.
"The ECFA will bring small enterprises closer to our Taiwan partners and make our cooperation more efficient," said Weng Rangui, who runs a large teashop at Maliandao Tea Market in downtown Beijing where he sells tea products traded with Taiwan partners.
"We will be able to share more profits with a larger market," Weng said.
Chen Zong-min, a businessman in Taiwan's fishing industry, shared a similar view with Weng.
"ECFA will promote a more convenient investment method for small and medium-sized enterprises on both sides, which on the long run will be good news for us," Chen said.
It is estimated that about 260,000 new jobs will be created in Taiwan by the ECFA's early harvest program, which will benefit at least 23,000 small and medium-sized enterprises in the island.