"Inuit were victims of misinformation and lies spread by a group that had no regard for their impact on our way of life," she said of Greenpeace's campaign against the seal hunt.
She did not specifically mention the issue of seismic testing to look for oil and gas reserves in Nunavut. Greenpeace opposes seismic testing and has been working with Inuit groups in Nunavut who are fighting federally-approved seismic testing off Baffin Island over concerns of the effects the tests would have on marine mammals.
Aglukkaq said Inuit need to stick together and not be manipulated.
"Other people who are not our friends will try to use Inuit as weapons in their own battles," she said.
"We have to think bigger than that. We have to ask, what are the battles that are important to Inuit. We have to ask how do we take control of our own future."
Aglukkaq spoke about her priorities as Chair of the Arctic Council, including making sure Northern people benefit from any resource development that happens in the region.
Prime Minister Stephen Harper also addressed delegates in a recorded message, in which he encouraged Inuit to take advantage of economic opportunities and to strive for healthy communities.