Gen Montoya is the 28th military official to lose his post over the scandal
The commander of the Colombian army, Gen Mario Montoya, has resigned following a scandal which tied military officers to the deaths of 11 civilians.
Three generals and 24 other soldiers have already been fired, accused of killing the men in order to inflate army statistics on rebel deaths.
The killings provoked a public outcry and an investigation is under way.
The UN has said Colombia must do more to address such killings, which it said are "systematic and widespread".
"I have passed 39 years in the service of my country and today I can say that journey has come to an end," said Gen Montoya.
He urged people not to judge the dismissed personnel without first giving them a chance to defend themselves.
Rights groups say the men who were killed were kidnapped or lured from slums in Bogota with the promise of work, before being killed in combat zones.
Last week, the government dismissed 27 military personnel, including three generals, 11 colonels, four majors, a captain, a lieutenant, and seven non-commissioned officers.
President Alvaro Uribe said a military inquiry had determined they had been guilty at least of negligence that included allowing "the collusion of members of the army with criminals" in "the murder of innocents".
11 young men disappeared from poor Bogota suburb in early 2008
Their bodies were found in mass graves near Venezuela border in August and September
Rights groups accuse the army of killing civilians to inflate successes
"We cannot allow any violation of human rights," he told a press conference.
One of the sacked officers, Gen Jose Joaquin Cortes, denied the allegations, telling Colombian radio: "I still absolutely believe in the innocence of my men."
The BBC's Jeremy McDermott in Bogota says the scandal appears to be part of a wider problem of what is known in Colombia as "false positives" - civilian deaths being claimed as rebels.
More than 2,300 members of the security forces or state functionaries are under investigation for such extrajudicial killings, says our correspondent.