2003–2004 Indonesian offensive in Aceh

On April 28, 2003, the Indonesian government issued an ultimatum to end the fighting and accept special autonomy for Aceh within two weeks. Free Aceh Movement (GAM) leaders based in Sweden refused the ultimatum, but the United States, Japan, and the European Union urged both sides to avoid armed conflict and resume peace talks in Tokyo. On May 16, 2003, the government stated that the offer of autonomy was the final concession it would make to GAM, and the rejection of the ultimatum would lead to military operations against the movement. GAM leaders and negotiators responded to this demand, and stated that its members in Aceh had been arrested while trying to leave for Tokyo.

After midnight on May 18, 2003, President Megawati Sukarnoputri gave the 12th Indonesian Military Chief, General Endriartono Sutarto, permission to commence military operations against the separatists. General Sutarto also imposed martial law in Aceh for a period of six months and the Indonesian government subsequently deployed 1,500 soldiers and 12,000 police to the province. This included a parachute landing by 458 paratroopers near Aceh airport.[4][5]

In June 2003, the government announced their intention to print a new ID card to distinguish all the people in Aceh from the rebels. NGOs and aid agencies were ordered to stop operations and leave the area and the government decreed that all assistance had to be coordinated through the government in Jakarta and the Indonesian Red Cross.

In May 2004, martial law in Aceh came to an end and the status of the conflict was downgraded to a civil emergency. Indonesian Coordinating Minister ad interim Hari Sabarno announced the change after a cabinet meeting on May 13, 2004. The government announced that they had made significant progress, and that during the operation thousands of GAM members had been killed, captured and surrendered.

Although martial law had been suspended, the military operations being conducted by the military continued. An estimated 2,000 people were killed during the fighting. According to Indonesian military sources, the majority of victims were soldiers, but international human rights groups and locals, including the government's human rights commission, claim that most of the victims were civilians. Evidence suggests that the military often does not distinguish between combatants, and non-combatants. Investigations also found GAM were responsible for the atrocities that occurred in Aceh.

Acehnese refugees in Malaysia have reported widespread abuses in Aceh, which was closed to observers during the military operation. The trial of members of the Indonesian military is considered difficult, and trials that have occurred have only involved low-ranking soldiers.

• Aceh Under Martial Law: Inside the Secret War (HRW report)