The conservation group says the latest numbers from the International Council for the Exploration of the Sea show significant population drops.
Federation spokeswoman Sue Scott says in North America, the total number of large salmon returning from Greenland last year dropped by 36 per cent to about 140,000.
She says the number of large salmon returning to Newfoundland was 20 per cent lower than the previous five-year average.
Salmon returns dropped most in the southerly part of their range. In the Penobscot River in Maine, for example, the numbers fell to 614 from 3,092 — a decline of 80 per cent, according to the latest council estimates.
Scott says one possible factor is Greenland's internal consumption harvest of 34 tonnes of Atlantic salmon last year, the second highest amount since 2001.
"Since 79 per cent of these fish are of North American origin, Greenland's fishery killed approximately 7,800 North American salmon," she said in a news release Thursday.
"This figure does not include unreported catches in Greenland, which are estimated to account for an additional 10 tonnes."
She is also concerned that Greenland allowed the sale of salmon to factories for the first time since 2001.
"This addition of factory sales is an incentive for Greenland to continue to increase its commercial fishery."
The federation is calling on Greenland to stop harvesting North American salmon, increase monitoring and stop sales of the fish to factories.
A request for comment from Greenland's fisheries minister was not immediately answered.
The latest annual report from the council, a network of more than 4,000 scientists, will be presented next week when the North Atlantic Salmon Conservation Organization meets in Drogheda, Ireland.
Concerns about the impact of open net pen aquaculture on wild salmon stocks will also be discussed.