Four of the crates were left in the ice, but one labeled Mackinlay's whisky was brought to the Canterbury Museum in Christchurch on New Zealand's South Island, where officials said Wednesday it was being thawed in a controlled environment.
Nigel Watson, executive director of the New Zealand Antarctic Heritage Trust, said the whisky might still be liquid.
"When the guys were lifting it, they reported the sound of sloshing and there was a smell of whisky in the freezer, so it is all boding pretty well," he said.
An Antarctic Heritage Trust team that was restoring the explorer's hut found the crates in 2006 but couldn't immediately dislodge them because they were too deeply embedded in the ice.
Drinks group Whyte & Mackay, the Scottish distillery that now owns the Mackinlay's brand, launched the bid to recover the whisky for samples to test and potentially use to relaunch the defunct Scotch.
Watson said the whisky may still be drinkable but would probably not be tasted.
"This was a blend so they are hopeful if there is enough alcohol left and it is in good condition they may be able to analyze and hopefully replicate the liquid so in fact everyone could partake in this," he said.
"It has been put on ice for 100 years so I don't think it is too unromantic a suggestion. The reality is that it is very limited quantities and our focus is on the conservation and not the drinking."
Shackleton's expedition ran short of supplies on its long ski trek to the South Pole from the northern Antarctic coast in 1907-1909 and turned back about 100 miles (160 kilometers) short of its goal.
The expedition sailed away in 1909 as winter ice formed, leaving behind supplies -- including the whisky and brandy.