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The ambitious journey is due to start next month, but Fiennes, 68, already in Antarctica, was injured after a fall while skiing during training at a base camp.
He developed frostbite after using his bare hands to fix a ski binding in temperatures of around minus 30C.
"This decision has not been taken lightly and it is, naturally, a huge disappointment to Fiennes and his colleagues," an expedition spokesman said.
Fiennes has already lost the tips of the fingers on his left hand to frostbite following a trip to the North Pole. He reportedly removed them himself with a fretsaw after learning of the cost and time it would take doctors to do it.
The Coldest Journey expedition - from the Russian base of Novolazarevskaya to the Ross Sea and close to New Zealand's Scott Base - is expected to take six months, facing some of the toughest conditions on earth - near permanent darkness and temperatures dropping close to minus 90C.
His remaining five teammates will continue with the 3219km trek, led by traverse manager Brian Newham.
They are due to leave on March 21, followed by two 20-tonne bulldozers dragging 140 tonnes of supplies.
The trek is known as The Coldest Journey on Earth. No human being has managed to walk across Antarctica in winter.
The journey is to benefit Seeing is Believing, a charity which tackles avoidable blindness, and aims to raise $US10 million ($A9.75 million).
Meanwhile, efforts to evacuate Fiennes to South Africa are being hampered by blizzard conditions. The team is trying to evacuate him by skidoo to the Princess Elisabeth Station and then to Cape Town.