In an unprecedented admission of guilt at the highest level of the Colombian military, the country's top commander, General Mario Montoya, resigned last Tuesday in response to public outrage over the army's extrajudicial killings of civilians.

Montoya's resignation follows last month's purging of 27 high-ranking soldiers, including three generals, for murdering civilians who were later claimed to be guerrillas killed in combat.

It is the first time the government has acknowledged allegations made by non-governmental organisations that its troops are killing non-combatants, who are then dressed in guerilla uniforms and presented as rebels, often complete with weapons or radios. The killings are carried out by soldiers under pressure from Bogota to increase the body count in the country's 40-year war against the leftist Revolutionary Armed Forces of Colombia, or Farc.

Farc, Latin America's oldest armed insurgency, demand land reform and wealth redistribution, and are locked in battle with government troops and right-wing paramilitary death squads. They have lost popular support thanks to their deep links with the country's 600-tonne-a-year cocaine trade and their use of extortion and kidnap.

Colombia was shocked when 11 young men reported missing from the Bogota suburb of Soacha early this year were found buried in mass graves in Ocana, near the border of Venezuela, in August and September.

In the days before Montoya's resignation, a United Nations official suggested international intervention was possible if Colombia did not investigate the case fully. Navanethem Pillay, the UN high commissioner for human rights, called such killings "systematic and widespread", and said failure to pursue the guilty could prompt international intervention.

The 11 men had been lured from their homes with offers of jobs and were later murdered, allegedly by army troops. It is not known if there was any connection between the victims.

"There may be members of the armed forces involved in murder and in failings of protocols and oversight," said President Alvaro Uribe, a Washington favourite and recipient of over $6 billion in US aid and military training and hardware under the controversial anti-drugs initiative Plan Colombia. The soldiers may now face criminal charges in civilian, rather than military, courts.

The head of Human Rights Watch's Americas division, Jose Miguel Vivanco, said the latest extrajudicial executions were not isolated events.

"It is a widespread and very serious nationwide problem," he said. "The attorney-general's office is investigating cases involving more than 1000 victims since 2003."

Defence minister Juan Manuel Santos has admitted that the body count mentality still pervades the army.

Amid opposition calls for Santos to resign, Uribe backed the minister, who he said was "pushing forward a solution to a very old problem, with many different roots".

This support for Santos will not be welcomed by any of the hundreds of Colombians who have lost relatives. Mariel Munoz, from the Meta province, southeast of the capital, lost her son, Jailler, when soldiers killed him in 2005 and presented him in Farc uniform with a radio and combat rifle. Her husband was murdered a year earlier in similar circumstances.

But Munoz is convinced her son was not a guerilla. She said: "He worked by his father's side every day. When he wasn't here, he'd tell me where he was. He was a decent boy. He hated the guerillas."

The move to purge the army of some alleged killers has been welcomed by human rights watchdogs, but they all say it is still not enough.

"It is a positive step - unfortunately, it is a very late step," said Vivanco. "For years, President Uribe has denied that there was any problem, instead accusing the organisations that reported the killings of furthering a guerrilla campaign to discredit the military. Such statements not only stigmatised human rights groups, but also allowed the killings to continue.

"It must do much more to look at all military units that have allegedly been involved in executions, and to ensure not only dismissals, but also full accountability for those responsible up the chain of command."

Many of the units implicated in the executions were trained, funded and vetted by US authorities, and the US should stop all military aid to Colombia, said John Lindsay-Poland, of New York's Fellowship for Reconciliation.

"In 2007 almost half these killings were committed by US-trained units. The unrestricted flow of US aid contributes to the impunity, because there is no consequence for their actions," he said.

The US announced on Friday that it would cut military funding of three battalions allegedly involved in the killings.

Human rights groups, however, claim that Montoya's replacement is also implicated in dozens of extrajudicial executions. General Oscar Enrique Gonzalez Pena was commander of the Fourth Brigade, based in Medellin from December 2003 to July 2005, when the army reportedly committed 45 extrajudicial executions in eastern Antioquia.

"The Colombian government presumably sought to replace General Montoya with an officer with a spotless record," said Lindsay-Poland. "But the reported executions of civilians under General Gonzalez Pena's command suggests that such high-ranking officers in the Colombian army are far and few between."