LIST OF WARS: DETAILS
Indonesia vs PRRI, Permesta and Darul Islam
Battle deaths: 33,965 
Nation(s) involved and/or conflict territory [note]
Indonesia, United States
During the Indonesian National Revolution, Kartosuwirjo founded his own band of freedom fighters in West Java, called Hizbullah and Sabilillah. As a protest toward the Renville Agreement signed by Indonesian leaders in 1948, which ceded West Java to the Dutch, Kartosuwirjo proclaimed a Darul Islam (meaning "Islamic State") in West Java on August 7, 1949. Darul Islam did not disband itself after the transfer of sovereignty in 1949, resulting in a clash with the government of the Indonesian Republic. Rebels in South Sulawesi led by army deserter Abdul Kahar Muzakkar joined the Darul Islam Movement in 1951. On 20 September 1953, Daud Beureu’eh declared that Aceh was part of the Islamic State of Indonesia (Negara Islam Indonesia) under the leadership of Kartosuwirjo.
Implementation of martial law in 1957, followed by declaration of Guided Democracy by Sukarno in 1959, marked the reversal of fortunes for Darul Islam. Smaller Darul Islam bands operating in Central Java under Amir Fatah was crushed by Colonel Ahmad Yani’s Banteng Raiders in 1954-1957. Darul Islam forces in South Kalimantan under Ibnu Hadjar was forced to surrender in 1959. Amir Fatah was killed in 1954, while Ibnu Hadjar was eventually executed in 1962.
Source: Wikipedia, published under the GNU FDL. Retrieved 2013-08-02
Two revolts against central Indonesian rule followed the proclamation of "Guided Democracy" by the Indonesian president Sukarno in February 1957.
Permesta was a rebel movement in Indonesia, its name based on Piagam Perjuangan Semesta (Universal Struggle Charter). It was declared by civil and military leaders in East Indonesia on 2 March 1957. The center of the movement was in Manado, and the movement was led by Colonel Ventje Sumual. Alexander Evert Kawilarang resigned his position as Indonesian military attache in the USA to become a general in the Permesta army. The Permesta rebels fought against central government troops until the last remnants surrendered and were given an amnesty in 1961.
The Revolutionary Government of the Republic of Indonesia (Indonesian: Pemerintah Revolusioner Republik Indonesia/PRRI) was a rebel movement led by army officers of the Indonesian Army. The rebellion included Dewan Banteng in Central Sumatra, Dewan Gajah in East Sumatra and Dewan Garuda in South Sumatra. In 15 February 1958 Lieutenant Colonel Ahmad Hussein declared the existence of PRRI.
CIA support of the Permesta rebels came in the form of 15 B-26 bombers and some P-51 Mustang fighters which formed the insurgent airforce AUREV (Angkatan Udara Revolusioner) based on Manado airfield, large amounts of weapons and equipment, significant funds, plus an international cast of CIA agents and mercenaries from Taiwan, Poland, the Philippines and the USA.
Responding to rebel and insurgent attacks, President Sukarno ordered the Indonesian military to crush the PRRI-Permesta rebellion. A series of air raids by the Indonesian Air Force (AURI) on Manado destroyed most of the rebel B-26 planes.
Meanwhile, a rebel B-26 bomber was shot down on 18 May 1958 by Indonesian pilot Ignatius Dewanto over Ambon. The B-26 pilot, the American CIA agent Allen Pope, was captured and exposed the CIA’s deep involvement in the rebellion. Consequently the CIA began to withdraw its support of the rebellion.
In August 1958 the PRRI rebellion ended and the government in Jakarta regained control of the rebel areas.
Indonesian troops quickly expelled the Permesta rebels from Manado, after which they maintained guerrilla resistance around the Lake Tondano area. However, the central government started a successful campaign offering amnesties to induce surrenders. Rebels who had many familial and amicable relationships with many of the central government soldiers began to surrender. The last Permesta rebels surrendered and swore an oath of loyalty to the central government in 1961.
This article was based on the following Wikipedia articles retrieved 2013-08-02: History of Indonesia, Permesta, PRRI
SOURCES: FATALITY DATA
 Battle deaths: PRIO Battle Deaths Dataset v3.0 (link) (1946-88) ID: #46
Low: 621 High: 34,444
NOTE ON NATION DATA
NOTE! Nation data for this war may be inconlusive or incomplete. In most cases it reflects which nations were involved with troops in this war, but in some it may instead reflect the contested territory.
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