The duo were arrested during a police raid on the headquarters of the newspaper in Abuja.
The police had said it obtained a warrant of arrest at the magistrate court in Wuse Zone 2, Abuja.
But vowing to investigate the raid, the human rights group called on government to ensure that the journalists have access to their lawyers and families.
Amnesty made its position known in series of tweets.
The arrest is coming on the heels of a petition written by Osuagwu Ugochukwu, counsel to Tukur Buratai, chief of army staff, alleging a “false and malicious story” written by the newspaper.
The army had written to PREMIUM TIMES, asking it to withdraw a report on Buratai being investigated by Code of Conduct Bureau.
Buratai had said the story received wide readership, and created bad image for him.
But PREMIUM TIMES stood by its story, vowing not to be intimidated. The newspaper in turn, demanded an apology from the army.
On Thursday, Musikilu Mojeed, editor-in-chief of the online publication, advised Buratai to go to court if he felt he had been defamed.
“We condemn this. It is an attack on press freedom,” Mojeed said.
“The army should stop deluding themselves that they can muzzle the press. Our loyalty lies with the people. We are not intimidated.
“The police came to our office because the chief of army staff complained that we defamed him. If he feels we have defamed him, he should go to court, and not raid a newspaper.”