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.
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.