On March 16, 2007, a Colombian military general named Henry William Torres Escalante gave the "direct order" to kill an unarmed farmer and his teenage son, dress them with weapons, and declare their bodies enemy combatants — in the sort of case that was repeated thousands of times in Colombia's war.

The ground troops under Torres Escalante's command in the 16th Brigade of the Colombian army were commended for their "good work," a mid-level officer later testified.

The army at the time was under intense pressure to boost combat statistics to prove that the government's campaign against Colombia's rebels was working. Two more men dead thus became two more dead rebels.

That case in the Casanare department, east of Bogota,is just one in a chilling string of so-called "false positive" extrajudicial killings that are haunting the country as it attempts to end 50 years of war.

On Wednesday, Human Rights Watch released a 95-page report on the practice, based on what it called previously unpublished documents and testimonies. The report directly names high-level military brass as responsible for at least 3,000 "false positive" killings between 2002 and 2008.

The scandal first became known in 2008, when a group of young men from a poor suburb of Bogotá were lured by recruiters with promises of work and then turned up in a mass grave, dressed as rebels.

"Committed on a large scale for more than half a decade, these 'false positive' killings constitute one of the worst episodes of mass atrocity in the Western Hemisphere in recent decades," says the HRW report, titled "On Their Watch."

Human Rights Watch researcher Max Schoening, and Americas director Jose Miguel Vivanco, speak in Colombia on the release of the report on false positives. (Photo by Leonardo Munoz/EPA)

The figure of 3,000 is based on open investigations being carried out by Colombian authorities, but the Human Rights Watch report warned that it "represents just a fraction" of alleged extrajudicial killings by the army during the two terms of former President Alvaro Uribe.

Uribe, now a senator who is protected with immunity under Colombian law, was president between 2002 and 2010. His government carried out a bloody, US-backed military offensive aimed at defeating and eliminating Colombian rebel groups, the largest of which is the Revolutionary Armed Forces of Colombia, or FARC.

As brigades faced pressure from above to dupe the numbers, the "false positive" campaign became "widespread and systematic," the report says.

The victims — often poor, disabled, or dependent on drugs — would be abducted or recruited with promises of work before being taken to remote areas and murdered in cold blood. Soldiers would then dress them in guerrilla uniforms and declare them combat kills.

While more than 800 low-level soldiers have been convicted for their involvement, no generals have faced justice. Some have even risen to the highest ranks of the military.

General Juan Pablo Rodriguez, current general commander of the armed forces, and General Jaime Lasprilla, the head of the army, both briefly led brigades that carried out extrajudicial murders, according to Human Rights Watch.

Colombia is investigating 22 generals for involvement, though no charges have been brought. Local media on Wednesday reported that the former army chief, General Mario Montoya, has been called to testify before a special prosecutor.

"It's very hard to believe army troops across the country were engaging in at least 3,000 of these killings over a seven year period with the same modus operandi without the knowledge or even orders of their commanders," Max Schoening, Colombia researcher for Human Rights Watch, told VICE News on Wednesday.

Troops who killed innocent civilians could expect to be rewarded with incentives such as time off or promotions. The report describes the case of a retired lieutenant, Marco Fabian Garcia, who was nominated for a medal of public honor and sent to a training camp — considered a privilege — for leading his troops in false positive killings.

"I did it because that's what they awarded me with," Garcia testified.

Gen. Juan Pablo Rodriguez, left, armed forces chief Gen. Leonardo Barrero, center, and President Juan Manuel Santos, in February 2014. (Photo by Fernando Vergara/AP)

President Juan Manuel Santos served as defense secretary at the time of the practice. The HRW report does not contain evidence against authorities above the ranks of the military.

On Wednesday, Santos criticized the report, saying it treats officials unfairly. "That is not the way to show respect for human rights," the president said.

Human Rights Watch urged the United States to place human rights conditions on further military aid to Colombia. Since the start of Plan Colombia in 2000, the US has sent more than $9 billion in aid to Colombia's armed forces for its efforts against guerrillas and drug traffickers.

The United States has consistently called Plan Colombia a success, and analysts call it a model for the Merida Initiative, the US aid package for Mexico. "The US should suspend the part of military aid that depends on Colombia's compliance with human rights conditions," the HRW report advises.

The release of the report is timely, given the government and the FARC's ongoing peace talks are currently negotiating how atrocities committed on both sides will be accounted for, in a future period Colombia is already referring to as "post-conflict."

While supportive of the peace process, Schoening said that if a deal is made with the rebels over past crimes, an unwelcome precedent will be set.

"If Colombia is going to offer lenient punishment for top guerrilla leaders guilty of war crimes, it's perfectly predictable that the military will demand that exact same level of leniency, including for horrendous crimes like false positives," he said.

The aim of the report, Schoening added, is to prevent that from happening.

"With or without a peace agreement, [we hope] these crimes are both investigated and prosecuted, and that all those responsible, including the top commanders, are punished with sentences that reflect the gravity of these crimes," Schoening told VICE News.