Armed riot police were present as a crowd of several hundred moved from Jordan to Mong Kok in the Kowloon district, staging what was intended as a "silent protest" against the planned law.
However, chanting and slogans were shouted towards police and later scuffles broke out in Mong Kok, prompting police to use pepper spray to subdue parts of the crowd.
Hong Kong Police said on Facebook that 53 people had been arrested and charged with unlawful assembly, adding that earlier some protesters tried to blockade roads in the area.
The proposed national security law has raised concerns among Hong Kong democracy activists and some foreign governments that Beijing is further eroding the extensive autonomy promised when Britain handed the territory back to China in 1997.
"The governments wants to shut us up and to kick us out," one protester, Roy Chan, 44, said. "We must stand up and strike down all those people who deprive Hong Kong people's freedom." Sunday's event came a day after Hong Kong police refused permission for an annual march usually held on July 1 to mark the 1997 handover, citing a ban on large gatherings amid the coronavirus pandemic.
China has said the new security law will target only a small group of troublemakers as it tackles separatism, subversion, terrorism and foreign interference in Hong Kong.
China's National People's Congress Standing Committee reviewed a draft of the bill on Sunday.
Chinese state media reported that lawmakers overwhelmingly supported the draft. The Chinese government has "unshakable determination to push ahead with enactment of the security bill and safeguard national sovereignty and interest," state broadcaster CCTV reported, citing a government spokesperson.
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