The three men -- a 22-year-old Jordanian, a 23-year-old Turkish citizen residing in Denmark and a 21-year-old Danish citizen who lives in Egypt -- were charged with the illegal possession of automatic weapons, The Copenhagen Post reported.
The Danish Security and Intelligence Service said in a statement the men are "suspected of having been in the process of preparing an act of terror."
"The investigation will establish whether possible terror threats have been addressed and averted by the arrests," the statement said, adding the men were arrested at two addresses in the Danish capital.
Kare Sorensen, a journalist for Jyllands-Posten, tweeted the newspaper is not believed to be the target of the alleged terror plot.
In 2005, Jyllands-Posten sparked international outrage among Muslims when it published caricatures of the Prophet Mohammed and has since been the target of several attempted revenge attacks, the BBC reported.
Four men are currently on trial for an attempted attack at the newspaper's office in Copenhagen in 2010.