The disappearance of the boys, aged between 11 and 15, sparked protests in the South American nation, which is in the throes of an armed struggle between narco gangs and security forces.
Saul Arboleda, Steven Medina, and brothers Josue and Ismael Arroyo were playing football in the western city of Guayaquil on December 8 when they went missing.
"The results of genetic forensic tests confirm that the four bodies found in Taura correspond to the three teenagers and a boy who disappeared after a December 8 military operation," Ecuador's prosecution service wrote on the X social media platform.
An unverified video released by Ecuador's Congress appears to show a group of soldiers putting one of the minors in a vehicle and beating him, while another was seen face down.
Defense Minister Gian Carlo Loffredo said that the soldiers, who had been on patrol, were responding to a request for help due to a robbery.
- 'Deeply regret' -
The incident led to widespread indignation in Ecuador, where kidnapping, extortion and murders are now commonplace.
The father of one of the boys said his family received a call the night of their disappearance during which Ismael was put on the phone. The boy said soldiers had chased them down, taken them and beaten them.
Later, the relatives received two locations via WhatsApp, one of them in the town of Taura, home to a military air base, and the other near a shrimp farm.
An anonymous caller told the family that criminals had taken the boys.
On December 24, the charred remains of four corpses were found near the Taura base, raising fears they were of the missing boys, though officials said at the time DNA tests were needed.
The prosecutors' statement on Tuesday confirmed that the bodies were of the adolescents.
Authorities early last week raided the Taura base and confiscated the phones of 16 soldiers suspected to be involved in the disappearance, as well as the vehicles used to transport the minors.
On Tuesday, the soldiers -- who had been put in military detention -- were ordered into custody by a criminal court.
They are being investigated for the forced disappearance of the boys, which carries a sentence of up to 26 years' imprisonment if they are convicted.
The soldiers claim they had released the boys in the area after a brief detention and that all four had been alive and in good condition at that time.
The Defense Ministry in a statement on behalf of the government, said "we deeply regret" that it has been confirmed that the bodies are those of the missing adolescents.
"We reaffirm our commitment to the truth, so that this case is handled with total transparency until we find those responsible for this murder," it added.
Dozens of relatives, neighbors and activists waving placards staged a protest outside a court demanding the soldiers be jailed.
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