Patrick Madahbee, grand council chief of the Anishinabek Nation, said in a statement there had been "numerous reports of racist commentary and incidents" across the country.
"Discussions about First Nations rights seem to bring out the worst in some Canadians," Madahbee said in a statement.
"We're seeking the assistance of teachers and school administrators to ensure that First Nations students entrusted to their care are not subject to any bullying or harassment."
Madahbee, who was in Ottawa, was not immediately available to discuss his statement.
About 70 per cent of 30,000 Anishinabek Nation students from 39 communities attend off-reserve schools in Ontario, said Murray Maracle, director of education with the Union of Ontario Indians.
Speaking on the grand chief's behalf, Maracle declined to discuss specifics of the problems, but did say there have been incidents of bullying and harassment against students.
He said the aim of the statement was to sensitize people to the situation.
"It's just to make administrators and people in those boards aware that this issue is happening," Maracle said in an interview from Curve Lake, near Peterborough, Ont.
The grassroots Idle No More movement, which has spread across the country in protest against what supporters see as a broken system of aboriginal governance in Canada.
A key complaint has been about a lack of consultation between the federal government and aboriginals on legislation, including the government's controversial budget-implementation bills.
Theresa Spence, chief of the troubled Attawapiskat First Nation in northern Ontario, has become a lightning rod for the movement since starting a high-profile protest near Parliament Hill last Dec. 11.
In recent days, someone desecrated a Tsuu T'ina flag about 40 kilometres east of Calgary.
The Idle No More movement had heightened attention to First Nations grievances, Maracle said.
The result was "small pockets" of people were taking out their anger or frustration on native students, he said.