Apple Daily on Thursday vowed to fight on despite another police raid and the arrest of several senior executives, saying staff will "loyally defend their posts".
In a letter to readers, the newspaper said every one of its journalists has reported the truth, legally and reasonably.
"Everyone at Apple Daily is upright. We will still try our best to be Hongkongers who persist, so that we can live up to the readers' [expectations]," the letter read.
Apple Daily said it had been left "speechless" by the government's warning for people to cut ties with the newspaper.
It said it has truthfully reported how other countries and various organisations have responded to the situation in Hong Kong, and these responses are facts available for the whole world to see.
The paper said police had taken away 38 computers used by journalists, proclaiming that "this is the worst era of Hong Kong!"
The Next Media Trade Union, meanwhile, said it was enraged by the national security arrests, saying editorial staff at the newspaper have always been professional and have stuck to journalistic principles.
It alleged that the case reflects an expansion of power by national security police, saying officers can now treat journalists as criminals and journalism as crime, merely by claiming that past news articles breached the law.
"This is a blatant violation of freedom of press in the name of national security. We would like to reiterate: journalism is not a crime," the union said in a statement.