"And I hope the Arctic will always showcase our ability to work together, not create new divisions."
Clinton said that representatives of various indigenous groups had contacted her to express their unhappiness that they had not been asked to attend the meeting.
Sweden, Iceland and Finland also voiced displeasure at their ommissions.
Indigenous groups and the three ommitted Arctic nations are part if the wider Arctic Council group that meets regularly.
Lawrence Cannon, the Canda foreign minsiter hosting the conference, said that those invited to the meeting had differentiated between the responsibilities of the Arctic coastal states and those of the Arctic Council, which the summit was not supposed to replace.
"As a matter of fact, I believe the deliberations today are very helpful to the Arctic Council and member states,'' he said.
Michael Byers, a professor of international law and politics at the University of British Colombia in Vancouver, told Al Jazeera that the three nations and indigenous groups should have been included.
"[Indigenous groups] should have been included as a minimum as observers and ideally as participants at the table so that their views could have been factored in in any decision making.
"We hope to see ever greater co-operation in the north [the Arctic], and co-operation involves building partnerships not closing doors."
The delegates from Russia, Denmark, Norway, the US and the host nation said on Monday they would said they would co-operate to map the area's seabed, regulate polar shipping and provide accident response.
"We are not reacting to change but shaping it," Cannon said after the meeting.
He said that the five nations had also reaffirmed their commitment to providing "an orderly resolution of any possible overlapping claims" to the Arctic's disputed areas.
They placed a "high priority" on a "mandatory regime for shipping in polar waters", which is expected to increase, Cannon said.
There are currently competing claims for territory in the Arctic region which is thought to contain undiscovered oil and gas reserves.
Russia is claiming a vast area across the central Arctic and the US is proposing extending its state of Alaska far to the north, both with claims lodged at the UN.
Canada, Denmark and Norway have also put forward proposals to extend their existing Arctic territory.
Byers said that shipping will become a key issue in the region and is potentially controversial.
"As the Arctic Ocean ice melts we are going to see 12-month per year shipping routes between Shanghai and Hamburg, or Shanghai and New Jersey," he said.
"The question is who will regulate those shipping routes, who will provide search and rescue, who will ensure that piracy will not become a problem in the Arctic?
"These issues over shipping and jurisdiction are much more controversial because the law on sea convention are not so clear on them."
Climate change in the Arctic is melting ice in the region, opening up waterways and providing access to huge mineral and petroleum wealth.