Some observers speculated that Hong Kong's pro-democracy "Occupy Central" protests that have blockaded key roads in the city for over six weeks since late September, may have been a reason for the delay.
The student led civil disobedience campaign pushing for full democracy, has been a thorny political challenge for China's Communist Party leaders and has posed the gravest governance challenge for Hong Kong since the city reverted from British to Chinese rule in 1997.
Xi's direct comments expressing support for the scheme, however, represent the most concrete sign so far that Beijing remains committed to this landmark move that could substantially expand the growth prospects for the two bourses.
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"I have long expressed to the central government that the sooner the Shanghai-Hong Kong Stock connect is launched, it will benefit both Hong Kong ...and the mainland's financial sector development," Leung said after his first formal face-to-face meeting with Xi since the political turmoil erupted in the city.
Chinese state news agency Xinhua cited Xi as expressing his support for Leung and his government's efforts to "safeguard the rule of law and maintain social order in Hong Kong".
"The rule of law is a key foundation for Hong Kong's long-term stability and prosperity," Xi said.
Beijing will "firmly support Hong Kong in developing democracy in line with law", he added.
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"The central government expects all circles in Hong Kong can ... seize the historic opportunity to realise universal suffrage according to the law and keep a stable, peaceful social environment for its citizens."
China has ruled Hong Kong since 1997 through a "one country, two systems" formula which allows wide-ranging autonomy and freedoms not enjoyed on the mainland.
Protesters are demanding fully-democratic elections for the city's next chief executive in 2017. Beijing has said it will allow a vote between pre-screened candidates.