Speaking at the opening of the annual National People's Congress, Premier Li Keqiang said calls from within the city to go it alone would "lead nowhere."
This was the first time "Hong Kong independence" has ever been mentioned in any Chinese premier's annual address.
"We will continue to implement, both to the letter and in spirit, the principle of 'One Country, Two Systems'," Li said, referring to the doctrine by which Hong Kong maintained certain freedoms and rights after it passed from British rule to Chinese in 1997.
"We pledge our full support to the chief executives and governments of (Hong Kong and Macau) in exercising law-based governance, growing their economies, improving people's wellbeing, advancing democracy and promoting social harmony," Li said.
Macau, a small island near Hong Kong, is also a special administered region of China.
He also had strong words for those who might seek independence for Taiwan. Officially the Republic of China, Taiwan has been self-governing since 1949, but Beijing claims it as an inalienable part of its territory.
"(China) will resolutely oppose and contain separatist activities for Taiwan independence," Li said. "We will never tolerate any activity, in any form or name, which attempts to separate Taiwan from the motherland."
Within Hong Kong, calls for independence from China have been growing since the 2014 Umbrella Movement protests
ended in no reforms to the existing political system.
For 79 days, thousands of protesters occupied Hong Kong's financial district and elsewhere to demand true universal suffrage -- one person, one vote, without the interference of Beijing.
The crowd was eventually dispersed by police, and organizers vowed to push for change by other means.
In parliamentary elections last year
, several pro-independence candidates were blocked from standing, but there was nevertheless a pronounced swing towards so-called localist parties, which support anything from greater autonomy to full self-rule
Two pro-independence lawmakers
who were elected never managed to take their seats however, having been ejected by the courts for failing to take their oaths of office properly after they staged a curse word-filled protest during the swearing-in process.
The intervention by Beijing into that case sparked more concerns by many Hong Kongers that the city's autonomy -- as guaranteed by "One Country, Two Systems" -- is being eroded.
Beijing has always reacted angrily towards any promotion of independence for its special administered regions of Hong Kong and Macau, or suggestions from self-ruled Taiwan that the island should seek full legal independence.
A bizarre propaganda video
posted online by the Chinese Supreme People's Procuratorate, the country's top prosecutor's office, in August contrasted apocalyptic images of Syria and Iraq with bucolic views of China today.
"The haze of 'domestic and international concerns' has not dispersed from the Chinese sky," the video said.
"Tibet, Xinjiang, Hong Kong and Taiwan separatism, as well as dissident leaders, lawyers who would fight until death and other agents of Western forces are damaging China's internal stability and harmony. Behind all these incidents, we can often catch a glimpse of the dark shadow of the Stars and Stripes."
Speaking to the South China Morning Post Sunday, political advisory body delegate Tam Yiu-chung said the mention of Hong Kong independence by Li shows that "Beijing is very concerned about the problem."
"The central government would not tolerate it ... it's a very serious problem," Tam said.
Some commentators have predicted that Hong Kong's next leader
, who will be chosen by a Beijing-dominated "election committee" later this month, will be told to crack down harder on pro-independence sentiment.
"(They) might be asked by Beijing to enact Article 23," Chinese University of Hong Kong professor Willy Lam told CNN last year, referring to a hugely controversial anti-subversion law that led to mass street protests in 2003 and the eventual resignation of then Hong Kong Chief Executive Tung Chee-hwa.