About 200 police raided the office of the Stand News online publication on Wednesday, froze its assets and arrested seven current and former senior editors and former board members.
The raid was the latest in a crackdown on the media and on dissent in general in the former British colony since China imposed a tough national security law in the city last year aimed at putting an end to months of pro-democracy protests.
The National Security Department of the police said in a statement on Thursday it had laid charges of "conspiracy to publish seditious publications" against two men, aged 34 and 52 respectively. Police did not identify the pair.
The same charge was extended to an online media company, it said, without identifying Stand News, in line with its practice.
"The other arrestees are being detained for further enquires," the department said.
Police earlier said seven people had been arrested "conspiracy to publish seditious publications".
Media said the seven were current and former senior editors and former board members of Stand News.
Media advocacy groups, some Western governments, including Canada and Germany, and the UN Human Rights Office condemned the raid on Stand News and the arrests as a sign of erosion of press freedom in the global financial hub.
Hong Kong returned to Chinese rule in 1997 with the promise that wide-ranging individual rights, including a free press, would be protected.
The city government's leader, Carrie Lam, said the action against Stand News was aimed at seditious activity not the suppression of the media.
"These actions have nothing to do with so-called suppression of press freedom," Hong Kong leader Carrie Lam told reporters.
"Journalism is not seditious ... but seditious activities could not be condoned under the guise of news reporting."
Set up in 2014 as a non-profit organisation, Stand News was the most prominent remaining pro-democracy publication in Hong Kong after a national security investigation this year led to the closure of jailed tycoon Jimmy Lai's Apple Daily tabloid.
Stand News shut down hours after the raid and all of its employees were dismissed. Its website was not accessible on Thursday and its London bureau chief, Yeung Tin Shui, said on Facebook his office had also closed.
Media said the two people charged were former chief editor Chung Pui-kuen and Patrick Lam, acting chief editor at the time of the arrest. They are expected to appear in the West Kowloon Magistrates' Court later on Thursday.
Four former members of the Stand News board - former democratic legislator Margaret Ng, pop singer Denise Ho, Chow Tat-chi and Christine Fang - remain in police detention. Chung's wife, Chan Pui-man, formerly with Apple Daily, was re-arrested in prison.
US Secretary of State Antony Blinken called on Chinese and Hong Kong authorities to immediately release those arrested.
Lam, referring to Blinken's call, said that would be against the rule of law.
The Chinese foreign ministry's Hong Kong office said support for press freedom was being used as an excuse to disrupt stability in the city.
"Those who engage in activities that endanger national security and undermine the rule of law and public order under the cover of journalism are the black sheep tarnishing the press freedom and will be held accountable," it said in a statement.
