Mahmudur Rahman, the editor of the Bengali-language Amar Desh newspaper was arrested during a raid on his office in Dhaka.
He faces charges including sedition and unlawful publication of a conversation that led to the resignation of the head judge of a war crimes tribunal.
The government has also accused Amar Desh of inciting violence.
But Islamist groups staged a street protest on Thursday against his arrest, describing him a "courageous and true soldier of Islam".
Mr Rahman has been remanded in custody by a Dhaka court for 13 days to allow police more time to interrogate him.
