President Clinton issued a classified directive in June 1995, Presidential Decision Directive 39, which said that the United States should “deter, defeat and respond vigorously to all terrorist attacks on our territory and against our citizens.”The directive called terrorism both a matter of national security and a crime, and it assigned responsibilities to various agencies.Alarmed by the incident in Tokyo, President Clinton made it the very highest priority for his own staff and for all agencies to prepare to detect and respond to terrorism that involved chemical, biological, or nuclear weapons.

During 1995 and 1996, President Clinton devoted considerable time to seeking cooperation from other nations in denying sanctuary to terrorists. He proposed significantly larger budgets for the FBI, with much of the increase designated for counterterrorism. For the CIA, he essentially stopped cutting allocations and supported requests for supplemental funds for counterterrorism.

When announcing his new national security team after being reelected in 1996, President Clinton mentioned terrorism first in a list of several challenges facing the country.