Archival records of the Department of Indian and Northern Affairs' Black Series (west of the border) and Red Series (East of the Manitoba-Ontario border) are a part of Library and Archives Canada Record Group 10. Included in these primary sources are files, letters, and correspondence related to administration for headquarters and the field offices.
Parts of the Library and Archives Canada collection have been digitized and may be searched and accessed online for free.
For information about RG10, see Indian Affairs Record Group 10 (RG10) Inventory
Suggestions for searching
1) Enter your key words - for example a personal name, an agency name, a band name, or a particular type of information (letter, treaty, etc.). It is not necessary to change the drop down box options - you may simply leave the setting at Any Keyword.
And then, if you wish...
2) You may limit results to items from the RG10 collection if you enter RG10 and select the option Archival Ref. Number in the drop down box. Be aware that information on your topic may be present in other RG collections, such as RG15 - the Department of Interior. ("As the primary agency responsible for the administration and development of all federal lands and natural resources in the former North-West Territories, the Department of the Interior played a significant role in the formation of federal scrip policy; in the creation and management of the scrip commissions; and in the administration of each commission's decisions concerning the awards given to individual Métis families. Given its mandate, it is only natural then that the majority of scrip commission records held by the National Archives should be found in the record group established for the Department of the Interior." For information on Metis Scrip Records in RG15, see here.)
Part of the Canadiana database is the collection titled Canadiana Heritage.
"The Héritage project is a 10-year initiative to digitize and make accessible online some of Canada’s most popular archival collections encompassing roughly 40 million pages of primary-source documents. Chronicling the country and its people from the 1600s to the mid-1900s, this collection represents a vast and unique resource for Canadian historians, students, and genealogists."
Check out the link to Learn More for help using the database. The link to What's coming on our catalogue may also be of use. It lists some content, whether finding aids, OCR searching and keyword indexing currently are available. The list is alphabetized - for example, on page 13, there are entries for the black series and the red series, with links.
Digitization work is ongoing - meaning it is not complete.
Also from the Canadiana Heritage link, there are links to collections titled Aboriginal History and Government Documents. Either of these also may be useful in your research.
Brandon University Library has a collection of microfilm titled Archival records RG10 from the Dept. of Indian Affairs - housed in the catalogued microfilm collection on the Main Floor of the Robbins Library - E78.C2P81. This collection is not complete. The Library has the following reels:
Volumes 3555-4095, reels C9639-9640, C10098-10187, C10190-10192, C10194-10198, C10203-10204, C11063 (index).
Volumes 6001-6491, reels C7908-7963, C8134-8219, C8639-8803, C9801-9811, C9641-9642 (indexes).
Volumes 999A-1728 (incomplete), reels C13900-13903, C13913-13936, C14250-14273, C14275, C14278-14280, C14297, C14838, C14865, C14866, T1455-1459, T1461, T1462, T1464, T1465, T1467-1476.
Volumes 1078-1133, reels C7208-7723, C8626-8636, C 9000-9009.