Protestors expressed particular concern about a lack of consultation.
"Basically consulation is being done after they drafted the legislation...they're doing it backwards," said Emily King, one of the demonstrators. "They should go to the communities because the communities know what's best for the children."
Anishinabek Nation Grand Chief Patrick Madahbee used a megaphone to speak to the crowd.
"This isn't just a one day rally here, we're going to be constantly working to eradicate this," he said. "There's been many times they've tried to ram this... crap down our throats and there's no damn way we're going to accept it."
"I know some of our leaders are (in the meeting)," he added. "But they're going in there because they're so desperately underfunded that they're trying to tell these people...change...what you're doing to our people."
Laura Calmwind from Kitchenuhmaykoosib Inninuwug was among the demonstrators who expressed concern about how the First Nations Education Act will affect treaty rights.
"It's going to undermine the treaty right to education," she said. "Because once you put a treaty (right) under legislation from another government, then you undermine the original relationship which was a treaty relationship between the British crown and Indigenous peoples."
"There's no...consent on my part for that legislation to be passed that will affect my children and my children's children," she added.
The protesters were later allowed to come in to the Aboriginal Affairs consultation meeting and make a deputation. They were asked to leave their signs at the door before heading in. Some protesters were told it was because of health and safety reasons.
A CBC reporter was asked by an Aboriginal Affairs official to leave the meeting.