Defense Minister Guillermo Botero quit his job Wednesday night after a senator from an opposition party revealed that at least eight children aged 12 to 17 were blown up by Colombia's military during an aerial raid against a criminal group's hideout on the edge of the Amazon rainforest.
The scandal has thrown Duque's already unpopular administration in disarray and further undermined confidence in the nation's armed forces, as they struggle to contain violence in remote pockets of Colombia's countryside.
"This leaves the president on very weak footing," said Jorge Gallego, a political analyst at Bogota's Rosario University. "It also reveals there are serious problems with how the Colombian military is conducting itself."
Duque, 43, was elected last year on a platform of reforming a 2016 peace accord with the leftist Revolutionary Armed Forces of Colombia, or FARC, and bringing order to areas of the countryside still troubled by the drug trade.
But the conservative president has struggled to contain criminal groups and dissidents of the peace deal that are now fighting over drug trafficking routes, illegal mines and other lucrative resources abandoned by the FARC guerrillas following their transition to civilian life.
Under Duque's watch at least 200 human rights activists have been assassinated across the country, according to INDEPAZ, an organization that monitors violence in Colombia. Dozens of former FARC rebels who laid down their weapons have also been murdered by criminal groups that are carrying out vendettas or seeking to enforce their control over former FARC territories.
Authorities say one of these criminal groups was headed by Gildardo Cucho, a former FARC rebel acting in line with a call by superiors to take up arms again, accusing the government of failing to fulfill promises made during the peace deal.
In late August the Colombian military bombed Cucho's camp in the southwestern province of Caqueta and announced the operation as a resounding success. "It was a strategic, meticulous impeccable and rigorous operation," Duque said after the bombing. Botero, who was then defense minister, also celebrated the bombing saying the country was "united" in its efforts to "defeat bandits."
The bombing made headlines for a day and then dropped off the radar for most Colombians. Then came the stunning revelations from Sen. Roy Barreras during a hearing Tuesday that among the bodies of those killed were numerous minors.
"That information was hidden from Colombians," Barreras said. "Minors were bombed and then re-victimized by being presented as criminals." Herner Carreño, a human rights official in Caqueta, said he had warned security forces that children in the area were being forcibly recruited by armed groups to work in their camps, including a 12-year-old girl.
Botero responded that his forces did not know there were children in Cucho's camp at the time it was bombed. However he did not clarify if he later found out that children had been killed. Colombia's congress was preparing to recommend his dismissal.
Patricia Muñoz, a political analyst at Bogota's Javeriana University, said Botero's resignation was long overdue. The minister had previously misinformed the country on an incident in which soldiers plotted the murder of an exxFARC rebel, saying the victim had died during a "scuffle" with police.
Under Botero's watch, Colombia's army commander also issued a controversial order to his troops to double the amount of rebels killed in military operations, which later had to be rescinded following a New York Times report.
Analysts say President Duque now faces the difficult task of recovering trust in the military and in his own administration as it faces complex security challenges. Gallego said Duque needs to start by appointing someone who is respected within military circles, and does not have a questionable human rights record. Botero had no experience with military affairs before being appointed as defense minister, but was a close ally of former President Álvaro Uribe, Duque's political mentor.
Gallego said the new pick of defense minister will signal if Duque is willing to chart a more independent course or is still "beholden" to the more conservative elements of his political coalition. José Miguel Vivanco, Americas director for Human Rights Watch, adds that Duque needs to oversee military promotions more carefully.
Earlier this year his administration promoted nine officers with questionable human rights records into key positions. "When you have those guys in top positions, I don't think it should be a surprise that we learn about these types of cases," Vivanco said.