In the footage the newspaper's chief editor Law Wai-kwong can be seen demanding a warrant from officers.
"Tell your colleagues to keep their hands off until our lawyers check the warrant," Law was filmed saying.
Apple's staff were ordered to leave their seats and line up so police could check their identities as officers conducted searches across the newsroom.
At one point 72-year-old Lai was present, in handcuffs and surrounded by officers.
In a statement police said the search was conducted with a court warrant which they said was shown to staff.
The security law was introduced in a bid to quell last year's huge and often violent pro-democracy protests, and authorities have since wielded their new powers to pursue the city's democracy camp, sparking criticism from western nations and sanctions from the US.
Lai's Apple Daily and Next Magazine are unapologetically pro-democracy and critical of Beijing.
Few Hong Kongers generate the level of personal vitriol from Beijing that Lai does.
For many residents of the city he is an unlikely hero - a pugnacious, self-made tabloid owner and the only tycoon willing to criticise Beijing.
But in China's state media he is a "traitor", the biggest "black hand" behind last year's protests and the head of a new "Gang of Four" conspiring with foreign nations to undermine the motherland.
Allegations of Lai colluding with foreigners went into overdrive in state media last year when he met with US Secretary of State Mike Pompeo and Vice President Mike Pence.