The samples were taken from the Huaorani ethnic group of about 3,000 people who live in a corner of Ecuador's isolated Amazon basin region, it is alleged.
The group is known for its unique genetic profile and immunity to disease, making it attractive to researchers.
The New Jersey-based Coriell Institute for Medical Research "eventually sold it in at least eight countries," Maria Del Pilar Troya, undersecretary of state for education and science, told AFP.
Germany, Brazil, Canada, the United States, India, Italy, Japan and Singapore were among the countries in which Ecuador believes the specimens were sold.
According to the Quito government -- which has strained ties with Washington -- more than 3,500 blood samples were taken over 30 years ago from 600 members of the Amazonian tribe.
The case arose following a 2010 complaint by a Huaorani Indian.
The Huaorani said they were told the blood samples were for medical tests for them, but the results never came.
"They took blood from the Huaorani, and in some cases, tissue samples. Hardly 20 percent of the people signed an authorization," Del Pilar Troya said.
The Coriell Institute told AFP that in 1991 it received one tube containing a particular cell line from a Huaorani individual's blood sample, the DNA from which has been used in scientific research.
Coriell said it had not drawn profit from the sample, and that the original has not been available for research since 2010.
At least two other US entities have been linked to the affair.