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“It is unfortunate that the Justice Department apparently violated its own guidelines, which indicate that such lists are to remain sealed to prevent unfair and un-American labeling of those who are not facing any criminal charges,” Mr. Ahmed said.

Conservative scholar Phil Kent said the Justice Department’s actions will “definitely hurt CAIR’s membership numbers in the future.”

“I’m not surprised to see these figures,” said Mr. Kent, who has written a book called “Foundations of Betrayal: How the Liberal Super Rich Undermine America.”

Mr. Jasser says some Muslims are hesitant to pay tithes to local imams or join organizations out of fear it may be linked to other groups that finance terrorism.

CAIR constantly notes in its press releases that it cooperates with federal law-enforcement activities and claims to conduct sensitivity training for Homeland Security officials. A February press release from CAIR’s Chicago office says it met with Homeland Security immigration officials and made an agreement to “conduct sensitivity training to [Immigration and Customs Enforcement] officers and possibly prison personnel.”

Homeland Security officials deny such claims and a check of the Office of Management and Budget Watch database of government contracts since 2000 shows CAIR has never been awarded a grant or a government contract.

“The department does not have a formalized relationship with that particular organization,” said one Homeland Security official speaking on the condition of anonymity. “We do have formalized relations with other community groups with whom we do contracts for training and consultation on matters that are specific to a given community.”

“It is not uncommon for that particular organization to issue a press release attempting to overstate their interaction with the department,” the official said.