But Alston said it was "unsustainable" for officials in Uribe's government to argue that the killings by troops seeking bonuses were carried out on a small scale.
He told Al Jazeera that the killings seemed to be "reasonably entrenched at least within the lower ranks of the Colombian military".
The UN envoy said the practice of "cold-blooded, premeditated murder of innocent civilians for profit" involved "a significant number of military units" in nearly half of Colombia's states.
"The sheer number of cases, their geographic spread, and the diversity of military units implicated, indicate that these killings were carried out in a more or less systematic fashion..."
UN rapporteur on extrajudicial executions
"The sheer number of cases, their geographic spread, and the diversity of military units implicated, indicate that these killings were carried out in a more or less systematic fashion by significant elements within the military," he said.
Colombia's chief prosecutor's office is investigating the deaths of 1,708 people who were executed and presented as guerrillas killed in combat over the past six years.
Alston also cited the case of at least 11 men and boys from the town of Soacha, outside the capital, Bogota, who were shot dead by soldiers last year and then passed off as rebels.
He told Al Jazeera that the government has acknowledged an official directive that indicated rewards would be paid to those who killed guerrillas in combat.
"Despite calls to eliminate that directive, it remains in force, although there is now an emphasis on capture rather than killing," Alston said.
"But you still have the very odd position of offering military members incentives for achieving goals in relation to the conduct of the war."
Alston said Colombia has taken important steps to stop and respond to these killings.
"But the number of successful prosecutions remains very low," he said.
Sergio Jaramillo, Colombia's deputy defence minister, said the country is also taking Alston's report very seriously.
He said the government was pleased that the UN official had recognised the "seriousness of the measures we've taken" to halt the killings and punish those responsible.