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 on Wednesday further raises concerns about media freedoms 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 had a warrant authorising it "to search and seize relevant journalistic materials".
"Over 200 uniformed and plain clothes police officers have been deployed," the statement said.
Separately, police said they had arrested three men and three women, aged 34 to 73, without naming them, for "conspiracy to publish seditious publications".
Ronson Chan, Stand News deputy assignment editor and the head of the Hong Kong Journalists Association, was not among those arrested, but said police confiscated his computer, iPhone, iPad, press pass and banking records during an early morning search of his residence.
"Stand News has always reported news professionally," he added. Other senior staff could not be reached for comment.
The Stand News office 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.
Officers were seen loading about three dozen boxes of documents and other materials seized as evidence onto a truck.
Steven Butler, Asia program coordinator for the Committee to Protect Journalists, said the police actions were an "open assault on Hong Kong's already tattered press freedom".
The government's Security Bureau did not immediately respond to a request for comment. Authorities have repeatedly said all prosecutions are based on evidence and had nothing to do with the profession of the people arrested.
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.
Authorities say the security law has restored order after often-violent pro-democracy unrest in 2019. Critics say the legislation is a tool to quash dissent and has set the global financial hub on an authoritarian path.
"When a free press ... is labelled 'seditious', it is a symbol of the speed at which this once great open international city has descended into little more than a police state," Benedict Rogers, chief executive of rights group Hong Kong Watch, said in a statement.
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 an additional "seditious publications" charge against Lai and six other former Apple Daily staff.
Police had not disclosed which Apple Daily or Stand News articles they considered seditious.
Local media said the six people arrested on Wednesday included former democratic legislator Margaret Ng, pop singer Denise Ho, former chief editor Chung Pui-kuen, acting chief editor Patrick Lam and former board members Chow Tat-chi and Christine Fang.
HKJA said in a statement it was "deeply concerned that the police have repeatedly arrested senior members of the media and searched the offices of news organisations containing large quantities of journalistic materials".
