A professor at Montana State University Northern filed a complaint against the school with the Montana Human Rights Bureau.
Yvonne Tiger, an adjunct professor, filed the complaint with the state agency, which is part of the Montana Department of Labor and Industry. Tiger is Native American.
Tim Little, an attorney with the Human Rights Bureau, confirmed the filing on Friday and said he could not comment on the details of the complaint.
"It is a race discrimination claim filed against MSU Northern," he said.
Tiger is the sole complainant.
MSU Northern has been the subject of scrutiny for its handling of a student's racist comments, which led to some Native American students feeling unsafe.
University administrators, led by Dean of Students Steven Wise, banned the student from campus but continued to let him play football. The student also went to live at Wise's private home, prompting criticism from professors and students.
Native American students at the Havre institution told The Gazette that racism is not a new issue at the school.
Wise, the dean of students, has yet to comment directly on his actions. But university Chancellor Greg Kegel has said administrators are reviewing their response and will be reaching out to various campus and human rights groups.
In an email to The Gazette on Tuesday, Kegel addressed the student living with Wise.
"Going forward, I will make it clear that there is no circumstance were (sic) university faculty, staff or administrators should be informally housing students," he wrote.
He also said that the university "has a lot of work to do" in its best practices with communication, including in student safety issues.
Little said that the Bureau has until June 14 to complete its investigation and issue a report. That deadline could be extended if the parties agree to mediation.