Enrique Eguime, an indigenous leader, had said the massacre took place in eastern Orellana when members of the Taromenane and Tagaeri peoples tried to stop a team of loggers from cutting down trees.
"We don't know the exact number of people killed, but there are also some children," Enguime said.
Xavier Garaicoa, the attorney-general, has called on other government authorities to confirm whether the massacre happened.
An investigating team made up of the leaders of several indigenous groups, is travelling in the Amazon jungle unarmed and without police escort.
"We're going in to investigate, but it's not going to be easy because of [the area's] remoteness," said Domingo Anguash, president of the Confederation of Indigenous Nations of the Ecuadorian Amazon.
Rafael Correa, the president, has vowed to protect Indian groups in the Amazon from oil development, illegal logging and poaching of rare tropical species.
The Taromenane and Tagaeri move around the 700,000-hectare Yasuni reserve the government has set aside as a protected area.
Ecuador wants rich countries to pay $350m a year for it not to extract 1 billion barrels of oil under the Yasuni reserve, where the tribe lives.
The country says leaving the oil in the ground would protect the environment in the Amazon, which would benefit all countries.