One of the men, David Headley, 49, was arrested on Oct. 3 and has been held without public notice since then, according to prosecutors in Chicago. Headley, a U.S. citizen was described as a convert to Islam, had an initial appearance in court on Oct. 11.
On the day before the arrest, a spokesman for U.S. Attorney Patrick Fitzgerald said he had no information on the case at the time.
The second man, Tahawar Rana, was arrested on Oct. 18 and had his initial court appearance that day.
In a statement, Fitzgerald said his office received permission from a federal court to hold the men in secret, "so as not to compromise further investigative activity."
Authorities say Headley "waived his rights" and has made statements to the FBI about his connection to the Pakistan terror groups.
The FBI arrested Headley at Chicago's O'Hare International Airport as he was about to board a flight to Philadelphia for an onward trip to Denmark.
FBI agents said he was carrying a copy of the newspaper, a street guide for Copenhagen, a list of phone numbers and a computer memory stick with ten short videos of the newspaper's offices and the entrance to a military barracks in Copenhagen.
Authorities said the plot against the Danish newspaper, Morgenavisen Jyllands-Posten, was referred to as the "Mickey Mouse Project" in communications between Headley and his contact in Pakistan.
Headley had already traveled to Copenhagen in January and visited two different offices of the newspaper, the FBI said.
His alleged co-conspirator, Rana, had reservations to fly to Copenhagen on Oct. 29, two days from today.
From Denmark, Headley then flew to Pakistan and met with his contact there, according to the complaint.
Authorities identified the contact as Ilyas Kashmiri, a commander of the Lashkar-4-Taiba group, which claimed responsibility for the Mumbai attacks.
Kashmiri recently told reporters in Pakistan that he supported al Qaeda and that attacks such as the ones in Mumbai will be "nothing compared to what has already been planned."
Headley, according to prosecutors, posted a message on an internet site in October, stating, "I feel disposed towards violence for the offending parties" for "making fun of Islam."
Other code words used for targets, according to authorities, included "investments," projects," business," and "action."
Headley is set to appear in court again Dec. 4.
This story has been updated.