JAKARTA – Soon after midnight on March 23, a group of heavily armed, masked men forced their way inside a prison near the Indonesian city of Yogyakarta and summarily executed four recently arrived detainees with gunshots to the head.

The coordination of the slayings, the professional demeanor of the masked men, and their military-style weapons and communications equipment prompted immediate speculation within the Indonesian news media and among human rights groups and lawmakers that the assailants were members of the military.

An uncharacteristically swift investigation by the army found that nine members of the army’s controversial Special Forces unit, known as Kopassus, were involved in the brazen prison shootings, while two others had come along in an attempt to stop their comrades. The army’s chief investigator in the case said April 4 that the soldiers had confessed to carrying out the shootings for revenge: The four detainees had been arrested in connection with the stabbing death of a Kopassus sergeant during a bar fight in Yogyakarta.

The prison raid has raised questions about what progress has been made in overhauling the Indonesian military since the collapse of President Suharto’s authoritarian rule in 1998 amid pro-democracy protests. During his 32 years in power and after, the military, and in particular Kopassus, has been linked to human rights abuses including extrajudicial killings, kidnappings and torture.

The shootings have also revived calls by human rights groups that the country’s laws be amended so that military personnel accused of serious crimes can be prosecuted in civilian courts, rather than in the military court system.

“We can’t rely on the military courts, which are already well known for not working properly in human rights cases,” said Haris Azhar, coordinator of the Commission for Missing Persons and Victims of Violence, a nongovernmental organization that documents military and police human rights abuses. “The military court is a dark room where the public and victims have little participation.”

Mr. Azhar cited cases in which military personnel received lenient sentences for serious offenses, as in 2003 when a military court sentenced four Kopassus soldiers who had been convicted of murder in the strangulation of Theys Eluay, a pro-independence leader in the restive eastern province of Papua, to prison terms ranging from three to three and a half years.

In 2011, a military court in Papua sentenced three army soldiers to terms of 8 to 10 months in prison for “abuse and insubordination” for beating and torturing two Papuan men to determine whether they were members of the Free Papua Movement.

Marcus Mietzner, a senior lecturer at Australian National University in Canberra and author of “The Politics of Military Reform in Post-Suharto Indonesia,” said the prison raid exposed a persistent culture of impunity within the armed forces and in particular Kopassus, because soldiers have little to fear from military courts.

Two weeks before the prison shootings, dozens of army soldiers attacked a police station in South Sumatra Province after the shooting of a soldier by a police officer, nearly burning it to the ground and wounding 17 police officers.

“There’s a pattern that whenever you have a member of T.N.I.” ? the Indonesian military ? “being hurt, injured or even killed, this kind of counterreaction is almost inevitable,” Mr. Mietzner said. “This was extreme, and because it was Kopassus, of course, it was extremely violent, but it’s not a new phenomenon.

“You can put it this way: It’s a welcome wake-up call to remind the public that military reform not only isn’t over, but in fact in terms of internal procedures, ethics, protocols and payments, it has yet to begin.”

While civil society groups praised the swiftness of the army’s investigation into the prison shootings, and the fact that the Central Java regional military commander was relieved of duty after asserting immediately after the shootings that soldiers had nothing to do with it, they are demanding that the assailants be tried in a civilian criminal court.

On Monday, however, Adm. Agus Suhartono, commander in chief of the Indonesian armed forces, rejected those calls.

“The law clearly states that it must be heard in a military court, so we will work according to the law,” he said.

Juwono Sudarsono, a former Indonesian defense minister and the first civilian to hold that post, said that before his retirement in 2009, he had negotiated with the House of Representatives on legislation that would allow joint military-police investigations of serious crimes involving military personnel and would establish a transitional period of five to eight years in which civilian and military legal procedures would be combined with sentencing by civilian courts.

He said that the civilian court system in Indonesia was too plagued by corruption and incompetence to handle trials of military personnel at that time, and that trying soldiers in civilian courts would exacerbate rivalries between the Indonesian armed forces and the national police at time when the country was less than 10 years into its democratic transition.

However, Mr. Sudarsono said, that bill was blocked because of opposition from the national police and human rights groups, which were pushing for more immediate civilian supremacy at the expense of the armed forces.

“But these nongovernmental organizations assumed that the police, the attorney general’s office and the courts were capable and clean,” he said. “I was vindicated, because neither of these civil authorities was capable nor clean.”

Sidney Jones, senior adviser to the International Crisis Group, a research organization based in Brussels, predicted that the military trials of the 11 Kopassus soldiers would probably be more open to public scrutiny given the news media attention surrounding the case.

“That will put more pressure on the military judges to give heavy sentences,” she said, “because if we look up till now at crimes committed by the military against civilians, it’s actually quite rare that they get sentences of more than four years when murder is involved.”

Yet there has also been an outpouring of public support for the 11 soldiers in Indonesian online chat groups and on news Web sites, because the four detainees they confessed to killing were widely believed to be gangsters involved in the narcotics trade in Yogyakarta.

“The majority of the reaction is for Kopassus,” said Yohanes Sulaiman, a lecturer at the Indonesian Defense University. “They are supporting the unit. They’re saying the police are incompetent and cannot control the gangs, so we need Kopassus to do extrajudicial killings.”