Prosecutors made the allegation in court papers as U.S. Magistrate Judge Nan Nolan prepared for a hearing to consider release of one of the men, Tahawwura Rana, on bond.
Prosecutors said Mr. Rana discussed with the other man charged in the case, David Headley, the possibility of an attack on the National Defense College of India.
The court papers did not provide more information on the alleged discussion and no other details were immediately available.
The document also said that Mr. Rana, who operates a Chicago immigration service, discussed the possibility of slipping people into the U.S. illegally with an unnamed individual belonging to a Pakistan-based terrorist organization.
Charges that the two men plotted to attack Danish newspaper Jyllands-Posten were unsealed last week by federal prosecutors. The newspaper sparked outrage throughout the Muslim world in 2005 by publishing 12 cartoons depicting the Prophet Muhammad. Muslims considered the cartoons extremely disrespectful.
Prosecutors have said Mr. Headley, whose former name was Daood Gilani, envisioned a plan to murder a cartoonist and the newspaper's former cultural editor.
Defense attorney Patrick Blegen has said that Mr. Rana--a Canadian national who was born in Pakistan and also owns a grocery store on Chicago's north side--was merely an innocent dupe of Mr. Headley or did not take Mr. Headley's plans seriously.
Prosecutors said the conversations about potential targets showed that Mr. Headley was serious.
Mr. Headley's attorney has said he has no comment on the case.