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The American Civil Liberties Union (ACLU) has long criticized the No Fly List and similar lists because of the lack of notification to persons included on such lists. The ACLU's stance is that the government has not provided a constitutionally adequate means of allowing individuals to challenge their inclusion on the list and that "constitutional rights are at stake when the government stigmatizes Americans as suspected terrorists and bans them from international travel."

In recent years, civil rights groups have filed lawsuits alleging that the government abuses the No Fly List to coerce Muslims into serving as informants. The ACLU has argued that the government "places people on the No Fly List based merely on a 'reasonable suspicion' that unconstitutionally vague criteria are satisfied. U.S. citizens and residents on the No Fly List are disproportionately Muslim and those of Arab, Middle Eastern, or South Asian descent."

Among the complaints about the No Fly List is the use of credit reports in calculating the risk score. In response to the controversy, Transportation Security Administration (TSA) officials said in 2005 that they would not use credit scores to determine passengers' risk score and that they would comply with all rights guaranteed by the First and Fourth amendments to the United States Constitution.

In the midst of this controversy, the Government Accountability Office of the U.S. Congress produced a report critical of the CAPPS II system. It characterized the proposal as incomplete and seriously behind schedule, and noted that the TSA had failed to address "developmental, operational, and privacy issues identified by Congress". On July 14, 2004, TSA officials announced that CAPPS II was being pulled from consideration without proceeding to full testing. Critics have alleged that the TSA has merely chosen to start with a less controversial entry point that they are calling the "Registered Traveler" program. TSA has also begun testing of another program called "Secure Flight", which is supposed to solve some of the problems of CAPPS I while avoiding the privacy issues of CAPPS II.

In January 2009, Marcus Holmes conservatively estimated the total cost of the program to be $536 million since 9/11, with a reasonable estimation range that approaches $1 billion, and he questioned whether the benefits of the list outweigh the costs.