The two will appear at West Kowloon Magistrates' Court on Saturday.
Apple Daily reported the two charged were editor-in-chief Ryan Law and chief executive officer Cheung Kim-hung.
On Thursday, 500 police officers raided the offices of the newspaper, arresting five executives and seizing evidence of articles the state alleges may have breached a national security law imposed by Beijing in 2020.
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.
It was the second time police have raided the Apple Daily headquarters; 200 officers went in last year to arrest owner Jimmy Lai on suspicion of colluding with foreign forces.