In a message to journalists, the armed forces said that the four soldiers from the group abducted on Sunday were freed on Monday, without giving details.
Indigenous Ecuadorans have been blocking roads in several provinces over the past week over right-wing President Daniel Noboa's move to slash fuel subsidies, which drove up the price of diesel by 56 percent.
The focal point of the protests has been the northern province of Imbabura, where a 46-year-old bricklayer was killed on Sunday.
The country's largest Indigenous rights organization, Conaie, said Efrain Fuerez, a father of two, was shot three times by soldiers and said it held Noboa responsible for his death.
A video released by Conaie showed a group of soldiers getting out of an armored vehicle and kicking two men on the ground, one of whom had gunshot wounds.
According to Conaie, the injured man was Fuerez, who later died in hospital.
The army has not commented on his death, which is being investigated by the attorney general's office.
Fuerez's widow Maria Lucila Guitarra said her husband was protesting the terrorism charges brought against 12 other protesters when he was killed.
"Mr Noboa, we are not terrorists," a distraught Guitarra said, adding that her husband was unarmed at the time of his death.
"He didn't even have a stick to defend himself," she said at her husband's wake at their home in a village in Imbabura on Monday.
The military on Sunday accused the protesters of injuring 12 soldiers and holding 17 others hostage.
A regional representative for the UN Human Rights Office called for "urgent dialogue" between the government and the protesters as well as a "thorough and transparent" investigation into Fuerez's death.
Conaie, which led mass protests that toppled three presidents between 1997 and 2005, has called for an indefinite national strike over the diesel price hike.
The US-backed Noboa has declared a state of emergency in eight of the country's 24 provinces, and a nighttime curfew in five of them.
He has claimed that Venezuelan criminal gang Tren de Aragua was behind the demonstrations, and has warned that protesters who break the law will be charged with terrorism and imprisoned for 30 years.