In a 95-page report, the rights group offers the most extensive look so far at the pattern of killings by the US-backed armed forces and the legal proceedings against military personnel who tried to present civilians as guerrillas killed in combat to inflate body counts, leading to promotions and bonuses.
While more than 800 soldiers have been convicted for such killings, most are low-ranking personnel. No charges have been filed against a single officer heading a brigade or anyone else higher up the chain of command at the time of the killings between 2002 and 2008 – the peak of the military offensive against the Revolutionary Armed Forces of Colombia.
Among the senior officers singled out by Human Rights Watch are two of Colombia’s most distinguished soldiers: General Juan Pablo Rodriguez, the current head of the armed forces, and General Jaime Lasprilla, the army’s top commander. Both led brigades in different parts of the country that were accused of carrying out at least 76 of the killings while briefly under their command.
“The generals are pretty much off the hook,” said Jose Miguel Vivanco, the Americas director for Human Rights Watch.
Colombia’s defence ministry has always denied it turns a blind eye to crimes committed by the country’s top soldiers.
Earlier this year, Chief Prosecutor Eduardo Montealegre said more than a dozen generals were under investigation, but so far none have been charged.
Human Rights Watch said Gen Lasprilla is not among those being investigated but Gen Rodriguez is. On Tuesday, Mr Montealegre’s office ordered four retired generals, including former army commander Mario Montoya, to provide testimony to prosecutors investigating the killings of civilians.
The rights group said that while senior officers were unlikely to have been directly involved in the so-called “false positives” killings, documents obtained by prosecutors show the officers signed off on troop movements and payments to soldiers and fake informants involved in the slayings.
That lack of scrutiny came in a period when reports were issued by the United Nations and others drawing attention to systematic executions taking place in several parts of Colombia.
President Juan Manuel Santos fired three generals and several other top commanders while serving as defence minister when the scandal broke. As president, he has expressed support for the investigations of army personnel.
But human rights groups want Mr Santos to go further, especially as he negotiates a peace deal with leftist rebels that in order to stick will require a crackdown on abuses committed by all sides during the country’s half-century-old conflict.
In addition to calling on the military to stop obstructing civilian prosecutors, Human Rights Watch’s report says more protection needs to be given to witnesses willing to implicate higher-ups in the face of death threats and other reprisals.