Capt. Jill Strelieff, public affairs officer for 1 Canadian Air Division in Winnipeg, said as the aircraft started sinking into the water, the already freezing hunters made their way through the frigid water to pull the pilot to safety.
All three men were taken to hospital and treated for hypothermia, but are listed in good condition. High winds made the temperature feel in the range of -50C.
The drama on the west shore of Hudson Bay began to unfold Tuesday night when the search was launched after the hunters didn't return home as scheduled.
Charlotte St. John said she was immediately worried for her brother Joe Karetak and his son Joe Jr., better known by his traditional name, Nepyok.
"Everybody knows all the seal hunters have to be back before dark, just for safety sake," St. John said.
At first, her uncle went out looking and found their abandoned snowmobile and sled. A small boat they had taken to retrieve their kill was gone.
She said local searchers tried to get the men by boat. "There's a lot of slush and the boats — they'd been trying all day to get to them — their engines freeze up."
Finally, a rescue crew in a military Hercules spotted the men about 4 a.m. and dropped them a radio and other supplies, she said.
Strelieff said on Wednesday, the military called in a civilian chopper pilot and asked him to go pick up the men.
Fears were briefly heightened when there were reports of a crash, but Strelieff said that's not what happened.
"There actually wasn't a crash," she said.
"A civilian chartered helicopter, a Bell Jet ranger from a local company, was going to rescue the two. When he landed on the ice floe, the weight of the aircraft broke through the ice and the two hunters were able to pull the pilot from the aircraft."
Strelieff said a large CC-130 Hercules aircraft from CFB Trenton was on hand and was able to parachute in two rescue technicians. The group of five then waited while a helicopter was dispatched from CFB Cold Lake in Alberta.
It managed to land safety and transported the entire group to shore. They were then transported to Arviat, Nunavut.
News the men were not seriously hurt was welcomed by Strelieff, who called it "fantastic.
"That's obviously what we can hope for in a situation like this."
She called the rescue-gone-wrong "an unfortunate incident and we're grateful all three individuals are in the best condition that you can expect at this time."
Search and rescue in the North is fraught with danger.
In 2011, a military search-and-rescue technician was killed while he and two of his colleagues were trying to rescue two men stranded in a boat in choppy waters in the Hecla Strait, 25 kilometres east of Igloolik, Nunavut.
The airmen had parachuted from a C-130 Hercules airplane to save the men and Sgt. Janick Gilbert died in icy waters before a rescue helicopter arrived to pick them up.
A preliminary flight-safety report into that incident said the tether designed to hold Gilbert's one-man raft to his life-preserver had separated at the threads and the raft was missing when he was found.