While confronting the crisis in the Congo and the escalation of the war in Vietnam, the Johnson administration simultaneously faced what it saw as the clear danger of communist takeovers in Indonesia and Greece. In both cases, American officials worried that instability, political immaturity, and misguided anti-American sentiment would lead a strategically and economically important nation to fall into the communist camp. The administration saw the military in Indonesia and Greece as the best alternative to this perceived threat and, therefore, welcomed their overthrow of the existing governments and their establishment of military dictatorships. The embrace of General Suharto in 1965–66 occurred without any opposition or much public notice in the United States as the rapid escalation of the war in Vietnam dominated America's concerns. The Vietnam War, however, would bring forth the first questioning of American containment policy and challenges to the policy of supporting authoritarian regimes. The political challenges to this policy were first manifested in 1967 in response to the Johnson administration's support of the colonels' coup and the overthrow of democracy in Greece.

American policymakers had worried since the late 1950s about the direction President Sukarno was taking Indonesia, but the situation became acute after 1963 as the Indonesian Communist Party (PKI) gained greater influence and Sukarno pulled Indonesia out of the United Nations, increased his criticisms of U.S. policy in Vietnam, confronted Great Britain in Malaysia, and aligned Indonesia with the People's Republic of China.