Since a reorganization in June 1996, KOPASSUS returned to the organization created in 1985. The stated reason for the reorganization was to permit a development rotation with one quarter on duty, one quarter in training, one quarter consolidation, and one quarter ready reserves which can be used at any time. Along with the reorganization and increase in size, its commander, the son-in-law of the Indonesian president, was promoted to two-star rank. By the late 1990s KOPASSUS numbered some 6,000-strong, an increase in the number of troops, but below that of 1985. Headquarters at Cijantung, East Jakarta, KOPASSUS had expanded to five Groups, with Group IV specifically handling intelligence operations along with the KOPASSUS Joint Intelligence Unit [SGI].While the "elite" corps of the Indonesian Army is the KOPASSUS Red Beret Corps with its special camouflage field uniform, there are many similarities among KOPASSUS, KOSTRAD, and other corps. Because of differences in units, however, there are individual improvisations that become special features of each corps. The KOPASSUS training package called "How to Find a Fine Fighter." With its headquarters in Cijantung, East Jakarta, KOPASSUS is considered to be an elite force that has traditionally emphasized its small size and its quick-strike potential. It has been involved in numerous military actions in response to internal Indonesian unrest. KOPASSUS units were involved in 1981 in freeing the hostages from the "Woyla," the Garuda Airline plane hijacked by followers of Imran, leader of an Islamic splinter movement in West Java. Imran forced the plane to land at the Don Muang Airport in Thailand. KOPASSUS troops to Thailand and brilliantly overwhelmed the hijackers. Around 90 troops from KOPASSUS were dispatched to Irian Jaya when a rebel group took hostages there have left the province without rescuing the remaining captives in 1996. KOPASSUS members climbed Mount Everest in 1997.
Colonel Prabowo Subianto, Suharto's son-in-law who married Siti Hediati Hariyadi Suharto in May 1983, was appointed to head KOPASSUS in December 1995. He was promoted to replace KOPASSUS chief Brigadier Subagyo Hadi Siswono, who was assigned to head the fourth Diponegoro Military Region Command.
On 15 July 1997 it was reported that Maj. Gen. Yunus Yosfiah, commander of the Indonesian Armed Forces [ABRI] Staff and Command College, replaced Lt. Gen. Syarwan Hamid as chief of ABRI sociopolitical affairs. Generally heads of ABRI sociopolitical affairs are officers with territorial, socio-political, or educational experience. Rarely if ever come from the ranks of the KOPASSUS Red Berets. Of previous heads including Bambang Triantoro, Sugiarto, Harsudiono Hartas, Haryoto P.S., Ma'ruf, Hartono, and Syarwan Hamid, not one came from the Special Forces Command. With the September 1997 appointment of Yosfiah as head of the sociopolitical affairs, the three top positions at ABRI headquarters were held by KOPASSUS Special Forces officers. ABRI Commander Gen. Feisal Tanjung, who was installed in 1993, was a KOPASSUS man, as was Lieutenant General Tarub, installed in 1997. This "domination" of the upper ranks at ABRI Headquarters has never happened in preceding periods.
KOPASSUS is associated with human rights abuses and "disappearances" which have been documented by respected human rights organizations and the Indonesian government. A number of activists were kidnapped by KOPASSUS troops in the last months of the Suharto regime, and at least 23 government critics disappeared. Nine later resurfaced and told stories of solitary confinement,interrogation, and physical abuse. One was found dead and 13 are still listed as missing. The abudctions took place ahead of a general assembly which reappointed Suharto as president for his seventh consecutive term on 11 March 1998.As of 01 April 1998 Lt. Gen. Prabowo Subianto [Suharto's son-in-law] was serving as commander of the Army Strategic Command [KOSTRAD] and Maj. Gen. Mukhdi Purwopranyono was serving as commandant of KOPASSUS. Suharto was ousted on 21 May 1999 amid mounting public pressure and large scale violent pro-reform riots. Soon thereafter Son-in-Law Prabowo was pushed out of his position as commander of KOPASSUS and reassigned to head the army's command and staff training college in Bandung. Armed forces chief General Wiranto set up the Officers' Honorary Council (DKP) on 03 August 1998 to probe the abduction and torture of scores of pro-reform political activists. On 21 August 1998 the Council ended its investigations of three senior officers linked to the kidnap and torture of political activists. In closed-door hearings, the Council questioned three officers from KOPASSUS, including the unit's former commander, Lt. Gen. Prabowo, son-in-law of ex-President Suharto. Wiranto admitted that KOPASSUS was involved in the kidnappings after the probe showed the KOPASSUS command had issued orders to "uncover several movements then considered radical and jeopardizing government programs and public security." On 06 April 1999 a military court on Tuesday found 11 members of KOPASSUS guilty of kidnapping nine pro-democracy activists and handed them jail terms of up to 22 months.
Maj. Gen. Mayjen Syahrir was appointed commanding general of KOPASSUS as of July 1998.Begining in early 1999 a campaign of systematic liquidation of the resistance was under way in East Timor, forcing thousands of people to flee into the jungles The operations were backed by at least a section of the Indonesian armed forces and intelligence service, notably KOPASSUS. In the countryside, village chiefs in favor of independence were systematically liquidated, and even villages considered not enthusiastic enough for autonomy were destroyed. East Timor resistance leader Xanana Gusmao accused a renegade "KOPASSUS old guard" of scorning Indonesia's avowed policy of curbing the violence in East Timor. Western military sources said known KOPASSUS officers were involved in attacks on the UNAMET compound in Maliana southwest of Dili, from where the UN subsequently evacuated all its local and foreign staff. In early August 1999, less than three weeks before the poll in East Timor on the territory's future, Indonesia's military commander there has been replaced by Col Muhamad Noer Muis, formerly of KOPASSUS. Most recently, Col Muis was the commander of war training in Sumatra. Jose Ramos Horta, Nobel Peace Prize laureate and a leader of the East Timor resistance, has claimed that the so-called pro-Indonesian Timorese militiamen are in fact members of KOPASSUS special passing themselves off as militiamen. The United States Congress developed over the past several years a compromise limiting International Military Education and Training (IMET) assistance to expanded-IMET, which is a human rights curriculum. However, the Department of Defense used Joint Combined Exchange and Training to train Indonesian military personnel in activities which would have been prohibited under the IMET ban, raising questions about a violation of Congressional intent.