"We must resolutely guard against overseas infiltrations via religious means and prevent ideological infringement by extremists," Xi told told a top-level meeting on managing religion in the world's most populous nation.
He laid out a broad guidelines under which millions of believers in China, including Buddhists and Christians, should carry out their faith without challenging the CPC's rule.
He said they should "merge religious doctrines with Chinese culture, abide by Chinese laws and regulations, and devote themselves to China's reform and opening up drive and socialist modernisation in order to contribute to the realisation of the Chinese dream of national rejuvenation.
His warning against infiltration through religion was seen as a reference to the role played by Christianity in the fall of Communism specially in erstwhile socialist countries like Poland.
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While China before the advent of Communist rule in 1949 was predominantly influenced by Buddhism which was brought to the country by eminent Chinese monks like Xuan Zang during the Tang Dynasty (618-907), Christianity has taken deep routes in the country in recent decades despite restrictions.
While Buddhism remained a dominant faith, Christianity is regarded as the fastest growing religion in Communist China.
Unofficial estimates said China has over 65 million Christians including Catholics, Protestants as well as other church groups. In view of restrictions and limited number of Churches, most of the Christians pray at home churches which are considered illegal.
The CPC has a tenuous ties with Rome apprehending political impact of the rapid growth of Christianity as it could become a movement in later years challenging CPC's power base. Both the Chinese government and the Rome recently made efforts to improve relations with positive messages from Pope and the Chinese government.
While asking religions to adhere to CPC rule, Xi promised to fully implement the Party's policy of religious freedom, manage religious affairs in line with laws, retain the principle of religious independence and self-administration, and help religions adapt to the socialist society, state-run Xinhua news agency reported.
"We should guide and educate the religious circle and their followers with the socialist core values, and guide the religious people with ideas of unity, progress, peace and tolerance," Xi said.
Religious groups, he said, shall "dig deep into doctrines and canons that are in line with social harmony and progress, and favourable for the building of a healthy and civilised society, and interpret religious doctrines in a way that is conducive to modern China's progress and in line with our excellent traditional culture.