The identity has not been released.
Marc Cornelissen and Philip de Roo were on a two-month scientific study of the area's ice for the Cold Facts organization. They are presumed to have fallen through ice and drowned near Bathurst Island, about 200 kilometres north of Resolute, at the end of April.
A dog that was travelling with the pair was located and rescued last weekend via helicopter.
In a news release issued Friday, RCMP said a team of local volunteers skilled in working in the area and dealing with poor ice conditions went to the location by snowmobile on Wednesday.
They recovered one body but could not locate the second missing man "despite their best efforts," said RCMP. Ice conditions were described as "very poor."
RCMP said the findings at the scene were consistent with both men perishing as a result of an accident.
The expedition is expected to return to Resolute today and the remains will be turned over to Nunavut's Office of the Chief Coroner for its investigation.