The warning comes as Scotland largest pig slaughterhouse has been forced to close due to a scarcity of the gas.
Carbon dioxide is used to stun the animals before they are killed, in an effort to minimise potential suffering.
It is also used to put the bubbles in fizzy drinks.
Supplies have dwindled across Europe as a result of operational problems at a key producer and maintenance shutdowns at other sites. Only one major plant is currently making the gas in the UK.
The shortage has already hit soft drinks and beer manufacturers, forcing some to cut production.
Now Quality Pork, a farmer-run co-operative abattoir in Brechin, has had to halt work until the situation is resolved. It processes around 6,000 pigs every week, providing meat to many major supermarkets.
Bosses there have warned the welfare of animals could suffer if the gas shortages continue, with farms in danger of over-crowding as pig numbers build up.
Andy McGowan is chief executive of the membership organisation Scottish Pig Producers, a partner in Quality Pork. He said the group has received no date when deliveries will return to normal.
“Short-term it will be OK, because there is a certain amount of spare capacity on farms, but the longer it persists the more serious it potentially gets,” he said.
“You can juggle things for a week or two but after that it starts getting a bit tricky.
“Eventually we will hit the stage where we have to get the pigs off farms.”
He warned that supermarkets could feel the effects of the gas shortages from next week, with fresh meat the first to be affected. Processed products such as bacon, sausages and ham could run low later.
And he has warned that other fresh meat and fish could also be hit as carbon dioxide is used as in the packaging process to extend shelf life.
Farmers have called for abattoirs to be prioritised when gas becomes available.
Penny Middleton, animal health and welfare policy manager for National Farmers Union Scotland, said: “Given the expectation of animal welfare problems on pig and poultry units, NFUS feels it is vital that CO2 supplies are reserved and directed to those plants in need.”
A spokeswoman for the Scottish Government said: “We are liaising closely with the UK government and industry bodies to share information and monitor the situation.”