Grants used for things like police training and communications systems are being canceled because of budget cuts on Capitol Hill.
The busy port city of New Orleans is on the list to lose money, which has leaders there questioning the decision process.
Cities considered main terror targets, including Los Angeles, New York, and Washington, D.C. and 29 other high-threat urban areas will keep receiving grants from the Department of Homeland Security.
The grant program was launched in 2003 in response to security threats in the wake of the terrorist attacks. Initially the money was available only to New York City, Washington, Los Angeles, Seattle, Chicago, San Francisco, and Houston. But since 2008 more than 60 cities have been awarded the risk-based grants.
The cuts come at a worrisome time for law enforcement. After the killing of Osama bin Laden, U.S. authorities have recovered evidence from his compound in Pakistan that the terror leader was encouraging his followers not to limit attacks to New York City, but consider other areas such as Los Angeles or smaller U.S. cities in future attacks.
The Associated Press contributed to this report.