The case of the children, aged 11 to 15, who went missing on December 8, has profoundly shaken Ecuador, with rights groups and the public demanding information about their whereabouts and asking that the case be investigated as a forced disappearance.
Authorities said 16 soldiers had been placed in custody and were being investigated for the disappearance of the minors.
Prosecutors said they are looking to charge some members of the military with forced disappearance in the case. T
According to a police official who spoke with The Associated Press, the bodies discovered Tuesday were found in a mangrove area near the western city of Taura, where the military base is located.
Two other officials following the case, told the AP the bodies were charred and showed signs of violence.
President Daniel Noboa, whose government has used the military to fight soaring crime as part of a security strategy with which he seeks to be reelected in February, has promised that his administration would not cover up for anyone in the disappearance.
The children went missing in the coastal city of Guayaquil, where dozens of people demonstrated on Monday demanding accountability and answers.
Defense Minister Gian Carlo Loffredo on Tuesday ordered the army to keep 16 soldiers in custody pending investigation, according to a statement posted on X.
Surveillance videos emerged this week showing men in military uniform grabbing two boys and driving off with them. The two are believed to be among four children who disappeared that night.
Loffredo on Monday confirmed the four were detained in the area where the footage was taken.
The videos, seen by the AP, show a group of children running, men in uniform, two children being placed in the back of a pick-up truck and the vehicle moving through the streets of Guayaquil. The footage appears to back up the account of Luis Arroyo, the father of two of the missing children.
Arroyo earlier told local media that his children were on their way home after playing soccer when two vehicles carrying people in military uniforms arrived in the area. The children, he said, were chased and four were caught and driven away.
Loffredo told reporters on Monday that, according to a military report, the children were detained by a patrol with 16 agents who "observed eight people who were allegedly robbing a woman."
He said the military later released the minors and did not hand them over to the police. The footage reviewed by the AP does not show the alleged robbery.