A draft had not been made public ahead of its passage, meaning the majority of people in Hong Kong have not seen details of a law that will now govern their lives.
The passing of the legislation has not been officially confirmed and details remain unclear. But RTHK reports that possible maximum sentencing for crimes under the law will be "much higher" than 10 years imprisonment.
Hong Kong's Chief Executive Carrie Lam refused to comment on the progress of the bill in her weekly press conference on Tuesday morning, saying it would be "inappropriate" to respond to questions while the NPC meeting is still in session.
China's State Council Information Office said it would will hold a press briefing on the national security law in Beijing on Wednesday morning.
The legislation was widely criticized by opposition lawmakers in Hong Kong, human rights groups and politicians worldwide, with many saying it will cement Beijing's direct control over the semi-autonomous city. Many worry it could be used to target political dissidents, activists, human rights lawyers and journalists amid the central government's continuing crackdown on civil society under President Xi Jinping.
The passing of the law comes a day before July 1, the anniversary of Hong Kong's handover from British colonial rule to China in 1997. It has become an annual day of protests in the city, but for the first time since handover police have not given permission to protesters to hold peaceful demonstrations.
The law's passing is expected to fuel further anger and protests in the city, which was rocked by over six months of increasingly violent anti-government unrest last year.
Crucially, those freedoms include the right to assembly, a free press, and an independent judiciary, rights that are not enjoyed on the Chinese mainland.
Chinese Communist Party officials and state media have defended the law as vital to protecting national security in the wake of last year's protests and a 17-year failure by the Hong Kong government to pass similar legislation, since the last effort was met with mass protests in 2003.
In a blueprint of the legislation revealed by Chinese state media Xinhua on June 22, mainland Chinese officials will be allowed to operate in Hong Kong for the first time and give Beijing the power to override local laws.
According to the blueprint, Beijing will establish a national security office, staffed by mainland security services to supervise local authorities in policing the law. A national security commission will also be set up, with a Beijing-appointed adviser and operating under "the supervision of the central government."
Additionally, Hong Kong's top official, the Chief Executive, will pick which judges hear national security cases, while mainland Chinese authorities will be able to "exercise jurisdiction" over cases in special circumstances -- a controversial clause that raises the prospect that certain crimes in Hong Kong could result in trials on the mainland.
Ultimately, the blueprint makes clear that national security law trumps local laws. If there is a conflict with existing Hong Kong law, the national security law will prevail.
He said Hong Kong "will continue to fight for our freedoms and democracy for the city's next generations. When justice fails, our fight goes on."
Following news of the legislation passing, Hong Kong democracy group Demosisto, which was formed as a political party by Wong in 2016, said it will "disband and cease all operation as a group given the circumstances."
It comes after Wong and other activist leaders, Nathan Law and Agnes Chow, said they would be withdrawing from Demosisto because of the threat posed by the law.
Wong and other activists have met with foreign diplomats and testified before the US Congress on Hong Kong's freedoms since the large-scale pro-democracy protests broke out last summer.
Rights group Amnesty International said the legislation "represents the greatest threat to human rights in the city's recent history."
"The speed and secrecy with which China has pushed through this legislation intensifies the fear that Beijing has calculatingly created a weapon of repression to be used against government critics, including people who are merely expressing their views or protesting peacefully," said the head of Amnesty International's China Team, Joshua Rosenzweig.
Taiwan's President Tsai Ing-wen said reports on China passing the security law "proves that 'one country, two systems' is not credible." Tsai said that Taiwan will start an office from July 1, which will "provide humanitarian aid for our friends in Hong Kong."
In Japan, Chief Cabinet Secretary Yoshihide Suga called the passing of the law "regrettable."
"As Beijing moves forward with passing the national security law ... We can no longer distinguish between the export of controlled items to Hong Kong or to mainland China," Pompeo said.
This is the first action the US government has taken to upend the special status trade relationship between the US and Hong Kong, following the determination that Hong Kong was no longer autonomous from China due to Beijing imposing the national security law on the city.
CNN's James Griffiths, Steven Jiang, Jadyn Sham, Eric Cheung, Nectar Gan, and Jessie Yeung contributed to reporting and writing.