Apple Daily, which posted on its Facebook page a livestream of police officers roaming through its newsroom and rifling through files, reported Jimmy Lai was taken away from his home early on Monday.
The live feed showed staff being asked to show identity documents. Some executive offices were sealed off with red cordons.
The police later wheeled in stacks of empty plastic containers.
Lai himself was brought back to the office later, initially in handcuffs.
"We can't worry that much, we can only go with the flow," Lai said, before being escorted into a police vehicle.
Police said around 200 officers entered the premises with a court warrant.
The law allows police to search premises without one "under exceptional circumstances", and also allows seizing documents, equipment, and financial assets.
The search was finished by midafternoon, and police said they collected 25 boxes of evidence.
Apple Daily reported one of Lai's sons, Ian, was also arrested at his home and later showed his restaurant, Cafe Seasons, being raided by police.
Shares of media company Next Digital, which publishes Apple Daily, plunged 16.7 percent before rebounding to trade 300 percent higher.
Some on Facebook posted screenshots of purchases saying they bought to show support for Lai.
Reuters was unable to verify the veracity of the posts.
“The market may now think the worst is over," said Kenny Ng, analyst at brokerage Everbright Sun Hung Kai.
Third world
An Apple Daily source said that other senior executives in the company were among those targeted and they were hiring lawyers. Next Digital Executive Director Cheung Kim-hung was seen escorted by police out of the building.