The warrant, which police said was aimed at gathering evidence for a case involving the national security law that Beijing imposed last year, raises further concerns about media freedoms in the Chinese-ruled city.
It was the second time police have raided the Apple Daily headquarters; 200 officers went in last year to arrest Lai on suspicion of colluding with foreign forces.
The security law was Beijing's first major move to set China's most restive city on an authoritarian path. It punishes anything Beijing deems as subversion, secessionism, terrorism and collusion with foreign forces with up to life in prison.
National security police said in a statement that five directors of a company had been arrested on suspicion of collusion with a foreign country or with external elements to endanger national security.