This is a list of activities carried out by the US Central Intelligence Agency in Indonesia.

Indonesia, pre–World War II Prior to World War II, Indonesia was a Dutch colony. The Dutch took control of the islands in the early 17th century and called it the Dutch East Indies. The Dutch held control over Indonesia until 1942, when the Japanese took control of the region. The Japanese controlled the region until 1945. In 1945, the Indonesians declared their independence from the Japanese empire. It took four years of rebellion and negotiations with the United Nations before the Netherlands finally recognized the independent status of Indonesia. The Dutch saw the US as a potential blocker in their attempts to regain control of the region, and the US had to play a large mediating role in Indonesia as they needed to appease the Dutch, the British, and the Indonesians themselves. This would prove difficult as the region became increasingly unstable during the period.

Indonesia, 1945–1950

Operation ICEBERG After World War II, six weeks after the atomic bomb was dropped on Japan, President Truman on September 20, 1945, signed an executive order to abolish the Office of Strategic Services (OSS) which took effect on October 1, 1945,Tim Weiner, Legacy of Ashes: The History of the CIA (New York: Doubleday, 2007) and temporarily the War Department was given control of the OSS branches that were still operational. Thus, departments were renamed to incorporate these new branches resulting in the Strategic Services Unit (SSU) and the Interim Research Intelligence Service (IRIS). These departments, along with military intelligence agencies, were put on the mission to collect information on surrendering Japanese troops and recovering military POWs and civilian internees. One recovery mission, known as Recovery of Allied Prisoners of War and Internees (RAPWI), had major complications because of the different approaches of the US, British, and Dutch allies. The humanitarian nature of these rescue missions provided cover for the CIA's real objective: to create a place to perform espionage in what would turn into the nation of Indonesia. The US did this out of fear for communist expansion in Southeast Asia, as it had already taken hold in the People's Republic of China. As Asia became a focal point for many conflicts, the native people of Indonesia came to realize that they were not helpless and their enemies were not invincible. Moreover, the US needed a "postwar central intelligence agency." According to the CIA online library, the US needed "a secret foreign intelligence service that preserved OSS's capacity to report 'information as seen through American eyes' and 'to analyze and evaluate the material for policymakers.' in southeast Asia".

At the time when operation ICEBERG was put into motion, Indonesia was still under control by the Dutch. Indonesians were against Dutch occupation as they had declared their independence in 1945. The U.S. had sympathy for the people of Indonesia and supported their independence. During this time, there was a violent four-year revolution in Indonesia that would eventually end with Indonesia free from Dutch Rule. In Batavia, the ICEBERG mission provided policymakers with information from the beginning of the revolution and how it evolved over the four-year battle.

Col. John G. Coughlin became the head of the planning of operation ICEBERG. He, along with the CIA, wanted to establish field stations in key cities such as Singapore, Saigon, and Batavia. Coughlin had an idea of four person teams each with specialists in espionage, counterintelligence, research and analysis that would make up the core of US intelligence stations across Southeast Asia. The stations' responsibilities included collecting information about Japanese war crimes, assessing the condition of U.S. property holdings, and accepting the surrender from the Japanese soldiers and commanders.

The Dutch did not want the US to establish an intelligence team in Batavia for many reasons. The first reason they argued was that it was not within "the sphere of influence" that the US had globally. The second reason they argued was that there was no need for the US to have intelligence there because they would only come up with the same intelligence that the Dutch and British had already acquired. The Dutch also stated that they along with the British would gladly inform the United States on anything they needed to know, but the British Southeast Asia Command (SEAC) had already given the go ahead for the US's participation in Batavia, so the Dutch were forced to allow the ICEBERG mission. Vice Adm. Lord Louis Mountbatten was the Supreme Allied Commander of SEAC and created a committee called "P" Division. The sole purpose of this division was to keep a watch on what the US was doing.

ICEBERG was commanded by OSS Major Frederick E. Crockett who arrived in Batavia on September 15, 1945, only one month after Japan intented to surrender and 13 days after Japan signed the instrument of surrender, which officially ended World War II. Crockett had traveled to Java aboard HMS Cumberland to head a two-teamed mission. Team A was located in the city of Batavia and their mission was espionage, counterintelligence, research and analysis, radio operations, and cryptography, and Team B was located in Singapore, and their mission was to be the backup to Team A if and when the time came.

Crockett also emphasized that the collecting of political and economic intelligence had to be carried out with extreme caution and a controlled nature. This was because the presence of the Dutch and British, whom he never had any intention of sharing his information with. Crockett only commanded the mission for a short period of time as the British asked for him to be removed. The British and the Dutch disapproved of the OSS's involvement in Indonesia and were in direct opposition to operation ICEBERG. The British successfully managed to remove Crockett from command after two months, citing that Crocket had been uncooperative to the SEAC. In Crockett's report, Crockett noted just the opposite: the SEAC had refused to give the OSS essential supplies, had commandeered OSS vehicles, and denied the OSS access to critical local fund. "Contrasted with wartime operations whereas an American unit we were recognized as a part of a team with a mutual objective," Crockett wrote in his conclusion about ICEBERG, "the Batavia mission could at no time be considered a joint and cooperative mission".

Director of the OSS, Major General William J. "Wild Bill" Donovan, was the mastermind behind operation ICEBERG. After World War II, General Donovan was of the opinion that the United States was behind other countries in terms of providing intelligence aimed at protecting and safeguarding the United States interest. On the back of this, Donovan informed President Truman that the United States required its own secret service agency to keep up with others and as a means to keep the United States adequately informed, towards the avoidance of surprise attacks and keep an eye on the Soviets' moves. Hence, the creation of the Office of the Secret Service.

At its inception, the OSS was primarily responsible for protecting the president from surprise attacks and assisting the United States in its Cold War struggle with the Soviets through the feeding of intelligence. However, through Donovan's orchestrations and vision, the OSS broadens its operation from the confines of providing secret service towards as direction of conducting covert and clandestine operations abroad. Coughlin had suggested to Donovan that the post war intelligence agency be much smaller than the OSS and employ only skilled agents. When the OSS officially disbanded in 1945, Donovan's intelligence career had officially ended. This being true, his ideas of a postwar intelligence agency had rooted themselves within stations in Southeast Asia. J. Edgar Hoover, FBI director, opposed Donovan's proposal of a postwar central intelligence agency because during the war, the OSS had become too close to the realm of responsibility occupied by military intelligence agencies, the FBI, and the State Department.

A major success of OSS intelligence came with the first American contact with Indonesian President Sukarno on September 27, 1945. Thanks to the Japanese occupation during WWII, the Indonesians were militarily trained and united as a country. Sukarno and his ministry promised their full support for the British occupation of Indonesia, but promised that if the Dutch attempted to occupy Indonesia, the Indonesians felt "capable of resorting to force if necessary in order to preserve their independence." This meeting, as well as other allied intelligence reports from around Java reporting resistance against the reinstatement of Dutch civil administration, surprised the British Southeast Asian Command (SEAC). The internal movement against the reinstatement of the Dutch government was far more widespread than the British or the Dutch had previously expected.

The liquidation of the OSS Effective October 1, 1945, President Truman signed an executive order that would dismantle the OSS. The responsibilities of the Intelligence Agency were transferred to the war department and was renamed the Strategic Services Unit (SSU). The OSS Research and Analysis branch was taken over by the State Department and renamed the Interim Research Intelligence Service (IRIS). Truman wanted James F. Byrnes (Secretary of State) "to take lead in developing a comprehensive and coordinated foreign intelligence program." This idea was resisted by State Department officials because they were against a centralized organization.

Although there was a transfer in Washington happening, the change had little effect on the efforts in Batavia. The OSS was simply replaced with SSU, and the growth of operation continued. Robert A. Koke was the most important SSU intelligence officer operating within Indonesia and was conducting clandestine missions in Southeast Asia longer than any American Intelligence officer. His responsibilities included training OSS agents and accompanying them on submarine missions. While he was not a full-time member of the ICEBERG mission his contributions made him an invaluable member of operation RIPLEY I. Operation RIPLEY was a covert operation which was orchestrated by the CIA which aimed to destabilize the Sukarno government during the Cold War era. The goal of this operation was to cause division in Indonesian politics through media campaigns and supporting anti-communist groups. The CIA provided funding, training, and logistical support to opposition groups and paramilitary organizations opposed to Sukarno's rule, leveraging existing tensions and grievances to undermine the government's authority. Additionally, the operation also looked to exploit internal divisions within the Indonesian military and exploit economic vulnerabilities to weaken Sukarno's grip on power.

The fate of HUMPY One of the objectives for operation ICEBERG was to discover the fate of J.F. Mailuku, an OSS wartime agent, who had been codenamed HUMPY. Mailuku studied engineering and eventually became an air force cadet in the colonial armed forces. Before the Dutch surrendered to the Japanese in 1942, Mailuku was evacuated to Australia, and from there he traveled to the United States. He was recruited and trained by the OSS and on June 23, 1944, he infiltrated Java via submarine for operation RIPLEY I.