In an interview with CBC Radio's All Points West on Tuesday, Justice Murray Sinclair told host Jo-Ann Roberts that commission staff has "seen the documents that relate to the experiments that were conducted in residential schools."
Other documents related to experimentation in aboriginal communities outside of residential schools have not yet been obtained, Sinclair said.
"We do know that there were research initiatives that were conducted with regard to medicines that were used ultimately to treat the Canadian population. Some of those medicines were tested in aboriginal communities and residential schools before they were utilized publicly."
Sinclair said some of those medicines developed were then withheld from the same aboriginal children they were originally tested on.
"Some of those medicines which we know were able to work in the general population, we also have discovered were withheld from children in residential schools, and we're trying to find the documents which explain that too," Sinclair said.
CBC News has not seen the documents in the possession of the commission.
Recent revelations that the Canadian government used at least 1,300 aboriginal children attending residential schools in British Columbia, Alberta, Ontario and Nova Scotia as test subjects have prompted further calls from aboriginal groups to pressure the federal government to turn over all archival documents related to residential schools.
A spokesperson for Bernard Valcourt, the minister of aboriginal affairs, called the nutritional experiments "abhorrent examples of the dark pages of the residential schools legacy."
"That is why we must continue the important work of reconciliation," Valcourt's office said.
The commission, according to Sinclair, is in possession of the documents used by historian Ian Mosby to show that the Canadian government conducted nutritional experiments on malnourished aboriginal children and adults attending residential schools during and after the Second World War.
However, the commission has not been able to obtain documents "related to experimentation that went on in aboriginal communities outside of the residential school setting."
"We haven't seen those documents," the chair of the commission told CBC News.
Valcourt's office has said they have turned over 900 documents related to this to the work by the commission.
Ottawa ordered to provide all documents
In January, an Ontario Court ordered the Canadian government to turn over all residential school archival documents to the Truth and Reconciliation Commission, and while the federal government has expressed a willingness to comply, Sinclair said "we haven't seen the documents start to flow yet."
The worry now, said Sinclair, is that even with the best of intentions Ottawa may not have the resources to provide all these archival documents in a timely manner.
"It's a question of capacity and whether they have sufficient resources and time to be able to get them to us before our mandate as a commission expires on July 1, 2014."
Sinclair said that if the federal government is unable to turn over all of the documents from Library and Archives Canada before the commission's mandate expires next summer, the commission may have to turn to the courts once more.
Many of the documents are said to reside with departments outside of Aboriginal Affairs, such as the Health Department.
But a final report without all the documents would not be a "truthful" report, according to Sinclair.
"The report itself, in our view, only complies with the mandate if we are able to write a full and complete history of residential schools and in order to do that, we need those documents," the chair of the commission told CBC News.
The residential schools system, which ran from the 1870s until the 1990s, removed about 150,000 aboriginal children from their families and sent them to church-run schools under a deliberate policy of "civilizing" First Nations.
Many students were physically, mentally and sexually abused. Some committed suicide. Mortality rates reached 50 per cent at some schools.
In the 1990s, thousands of victims sued the churches that ran the schools and the Canadian government.
The $1.9-billion settlement of that suit in 2007 prompted an apology from Prime Minister Stephen Harper followed by the creation of the commission in 2008.
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