"We're going all out! This war against the bad guys will intensify," the ministry said in a social media post, announcing the deployment of special forces, intelligence and counterterrorism forces.
Ecuador on Friday revealed that at least 11 troops were killed in an operation to combat illegal mining in the jungle near Ecuador's border with Peru.
Quito blamed the attack on dissident factions of Colombia's FARC, once the largest guerrilla group in Latin America, that operate across the area.
The guerrillas allegedly attacked with explosives, grenades and firearms, causing one of the worst tolls in recent years.
The attack has shocked Ecuador and prompted three days of national mourning.
Ecuador had averaged a killing every hour at the start of this year, as cartels battled for control over cocaine routes that pass from Peru and Colombia through the nation's ports.
Ecuador's prosecutor's office blamed the guerrilla attack on the FARC offshoot Comandos de la Frontera.
After Colombia's peace process led to the demobilization of FARC in 2017, the Comandos de la Frontera rearmed.
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