Keck said that after the database is shut down, a copy of the data it contains will be maintained at the Pentagon for record-keeping purposes, but not for further analytical use.
The decision to end the program, which had been recommended in April by the Pentagon's new intelligence chief, James R. Clapper Jr., was approved by Deputy Defense Secretary Gordon England, Keck said.
The American Civil Liberties Union, a chief critic of the program, applauded the Pentagon's announcement. "It was high time for this program to be shut down," said Anthony D. Romero, executive director of the ACLU. "There should be no place in a free democratic society for the military to be accumulating secret data on peaceful demonstrators exercising their First Amendment rights."
The program, known as TALON, was created after the Sept. 11, 2001, terrorist attacks and was designed to maintain a base of information on potential threats to military facilities and personnel.
In December 2005, it was disclosed that the system included data on antimilitary protests and other peaceful demonstrations.
Antiwar groups and other organizations -- including a Quaker group, the American Friends Service Committee -- protested after it was revealed that the military had monitored antiwar activities and organizations and individuals who attended peace rallies.
Pentagon officials have said the program was productive and had detected international terrorist interests in specific military bases. But they also acknowledged that some officials may not have been using the system properly.
The TALON reports are kept in a large database and analyzed by an obscure Pentagon agency, the Counterintelligence Field Activity, or CIFA.