The entire population of Minnesota was enumerated by the US and Minnesota Territorial/State Census, but in 1885 the Bureau of Indian Affairs (BIA) also started taking a separate Indian Census. BIA agents were supposed to record all Indian reservation residents each year, but some tribes were exempted from this law and some agents did not create records annually. This separate Indian Census continued until 1940.
In addition, there were a number of other census, annuity, and other lists of American Indians living in Minnesota that were created over time.
In general the U.S. Indian Census Rolls can be searched through Fold 3 or Ancestry.com. (Access to these databases requires a subscription, but visitors to the MNHS Library can use our subscription for free.) They are also available for browsing/viewing online for free through the Internet Archive.