The attack on Friday comes amid a spike in violence in both nations linked to the trafficking of cocaine produced in Colombia and exported through Ecuadoran ports to the United States and Europe.
Around 80 soldiers were carrying out an operation to combat illegal mining in the Ecuadoran Amazon when they were attacked by the guerrillas, leaving 11 soldiers and a militant dead, and one soldier wounded, Ecuadoran officials said.
The Ecuadoran military said in a statement Friday that the "ambush" had been carried out with explosives, grenades and firearms.
"We will find those responsible and we will finish them off," Ecuador's President Daniel Noboa said on social media platform X.
The national mourning period in honor of the slain soldiers will run through Monday, according to the presidency.
The office of the prosecutor said a criminal offshoot of FARC called the Comandos de la Frontera, or Border Commandos, was responsible for the attack in the eastern province of Orellana.
Some armed factions within FARC, once the largest guerrilla group in Latin America, have rejected its historic peace agreement made with the Colombian government in 2016.
Those splinter groups refuse to lay down their arms and pursue criminal activities like illegal mining and drug trafficking.
Comandos de la Frontera is involved in drug trafficking in the border region of Colombia and Ecuador.
The prosecutor's office said that work had begun to "recover the bodies and secure evidence" at the site of the attack.
According to Mario Pazmino, a retired colonel and former head of army intelligence, the area is a "sanctuary for organized crime" where Colombian, Ecuadoran and Brazilian groups operate.
After the demobilization of FARC in 2017, the Comandos de la Frontera were able to rearm in about a year and a half and their expansion has accelerated, Laura Bonilla, a researcher at the Peace and Reconciliation Foundation, told AFP.
"Neither the Colombian nor the Ecuadoran state has been able to guarantee a state presence that provides security, justice or protects the territory from the presence of armed groups," she added.
Colombian Defense Minister Pedro Sanchez said the deadly attack on Friday demonstrated the threat posed by organized armed groups.
"Their criminal violence is unacceptable and must be confronted with the full force of the state," he wrote on X.
The Ecuadoran military said it would "not rest until those responsible are judged before the law and are held accountable."
- A killing every hour -
Once-peaceful Ecuador averaged a killing every hour at the start of the year, as cartels battled for control over cocaine routes that pass through the nation's ports.
Despite President Noboa's tough-on-crime policies, the country has the highest murder rate in Latin America.
There are 40,000 gang members in Ecuador, the president has said -- almost double the 22,000 narco traffickers and rebels in Colombia, according to official figures.
The bloodshed in Ecuador has spooked investors and tourists alike, fuelling economic malaise and swelling the ranks of the nation's poor to 28 percent of the population.
In Colombia, the Comandos de la Frontera are engaged in peace negotiations with authorities, with a further round of talks set for later this month.
The United States is seeking the extradition of the group's detained leader on drug trafficking charges, Colombian officials have said.
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