"We will resolutely contain the 'Taiwan independence' secessionist activities in any form," Xi told a group of lawmakers from Shanghai on the first day of the national legislature's annual session.
This was first such warning issued by Xi after the Tsai Ing-wen was elected as President defeating pro-China Kuomintang party candidate Eric Chou in January elections.
Chou was backed by former Taiwanese President Ma Xiaoguang, who met Xi at a well publicised meeting in Singapore and agreed to improve ties between China and Taiwan, which broke away from China in 1949. China says Taiwan is part of it.
"It is the common wish and firm will of all Chinese people, and it is also our solemn commitment and responsibility to the history and the people," he said.
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"Our policy toward Taiwan is clear and consistent, which will not change along with the change in Taiwan's political situation," Xi told the lawmakers.
Only by accepting the historical facts about the "1992 Consensus" and recognising its core implications can the two sides have a common political foundation and maintain good interactions, Xi said.
"We will adhere to the '1992 Consensus' as a political foundation, and continuously advance the peaceful development of cross-Strait ties," Xi added.
Premier Li Keqiang also warned against "separatist activities" on the island and pleded to safeguard China's "territorial integrity".
China will "oppose separatist activities for the independence of Taiwan" and "safeguard China's sovereignty and territorial integrity", Li told the Communist-controlled legislature.