Civil libertarians, librarians, and others have protested changes made by the act that have the potential to lead to law-enforcement abuses, including reduced judicial oversight of wiretaps, expanded law-enforcement access to records held by third-party businesses and organizations, and an ambiguously broadened definition of providing material support to terrorists. Such concerns have been partly prompted by the fact that the USA PATRIOT Act was designed in part to reduce restrictions enacted in response to abuses of government power associated with Watergate, anti–Vietnam War protesters, civil-rights groups, and the like.

These worries contributed to the vocal opposition in 2003 to the Bush administration's draft Domestic Security Enhancement Act, an expansion of the USA PATRIOT Act that ultimately was not submitted to Congress. Similarly, the renewal of those sections of the act slated to expire at the end of 2005 became contentious enough that opponents in the Senate were able to stall legislation to make them permanent, but after some modifications were made to the act in 2006, the act was renewed and most sections became permanent. Aspects of the law have been challenged in the courts, with varying results.