Stand News, set up in 2014 as a non-profit, is the most prominent remaining pro-democracy publication in Hong Kong after a national security probe earlier this year led to the closure of jailed tycoon Jimmy Lai's iconic Apple Daily tabloid.
The raid further raises concerns about the freedom of speech and that of the media in the former British colony, which returned to Chinese rule in 1997 with the promise a wide range of individual rights would be protected.
Police said in a statement it was conducting a search with a warrant authorising it "to search and seize relevant journalistic materials".
"Over 200 uniformed and plain clothes police officers have been deployed during the operation. The search operation is underway," the statement said.
Senior Stand News staff could not be reached for comment.
Sedition is not among the offences listed under the sweeping national security law imposed by Beijing on the city in June 2020 that punishes terrorism, collusion with foreign forces, subversion and secession with possible life imprisonment.
But recent court judgements have freed authorities to use powers conferred by the new legislation to deploy previously sparsely used colonial era laws, including the Crime Ordinance which covers sedition.
In June, hundreds of police raided the premises of Apple Daily, arresting executives for alleged "collusion with a foreign country". The newspaper subsequently shut down after police froze its assets.
On Tuesday, prosecutors filed a "seditious publications" charge against Lai and six other former Apple Daily staff, adding to the earlier charges. The charge sheet said their publications could "bring into hatred or contempt" or "excite disaffection" against the Hong Kong and Chinese governments.
Police had not disclosed which Apple Daily or Stand News articles they considered seditious.
The Stand News charter states that it shall be independent, autonomous and committed to safeguarding Hong Kong's core values of "democracy, human rights, rule of law and justice".
After the Apple Daily raid, Stand News said it would stop accepting donations from readers and had taken down commentaries from the platform to protect supporters, authors and editorial staff, adding that "speech crimes" had come to Hong Kong.
Local media said the six people arrested on Wednesday included Ng, Ho, Chung, acting chief editor Patrick Lam and two former board members Chow Tat-chi and Christine Fang.
Stand News posted a video of police arriving at the residence of Ronson Chan, its deputy assignment editor who is also the head of the Hong Kong Journalists Association.
"The charge was conspiracy to publish seditious publications. This is the court warrant and this is my warrant card. Your phone is obstructing our work," an officer is seen saying.
Local broadcaster Cable TV said Chan was not arrested and only assisting the investigation.
Police said in a separate statement that they had arrested three men and three women, aged 34 to 73, and that searches of their homes were underway. It did not name those arrested, in line with its usual practise.
The Stand News bureau in an industrial building in the Kwun Tong working class district was partially sealed off, with scores of police milling about the lobby and four vans parked downstairs, according to a Reuters reporter at the scene.
A police media liaison officer on the 14th floor said entry to the office would not be permitted given an “ongoing operation”.