There were about "3,500 procedures" in which blood was drawn without authorization from 600 Huaorani, who live in a corner of Ecuador's isolated Amazon basin region, said Rene Ramirez, head of the Higher Education and Science Ministry.
Samples "were also taken from some people on more than one occasion", he said, revealing new details of a government investigation, on state television ECTV.
In the initial report two years ago, the Huaorani, whose language is not clearly linked to those of local Quechua-speaking indigenous people, said some US people duped them in 1990 and 1991.
The Huaorani said they were told the blood samples were for medical tests for them, but the results never came.
When the allegations emerged in 2012, the US embassy said it was not aware of the case. On Monday, as new details emerged, a US embassy spokesman did not immediately respond to requests for comment.