The retailer, which supplies restaurants and bars, is limiting orders to 10 cases of beer and five of cider or soft drinks, the BBC has reported.
Booker said in a statement: "Due to the international shortage of CO2, we are experiencing some supply issues on soft drinks and beer.
"We are currently working hard with our suppliers to minimise the impact for our customers and cannot comment further at this stage."
As revealed by trade title Gas World, the meat and drinks industries have been hit by a Europe-wide shortage of CO2 as a number of manufacturers have closed for seasonal maintenance.
Food-grade CO2 is used to add fizz to soft and alcoholic drinks, and as a “humane” method of stunning pigs and chickens prior to slaughter.
Scotland’s largest pig processing plant, Quality Pork Limited in Brechin, Angus, suspended its slaughtering process on Tuesday due to a shortage of the gas, according to The Herald.
Pubs are already seeing deliveries of Heineken’s Amstel and John Smith’s Extra Smooth beers disrupted amid a period of high demand due to the World Cup.
Coca-Cola Great Britain has temporarily paused some production lines, but the company said there was no disruption to supply.
The industry is hopeful that food-grade CO2 production will begin to return to normal in early July.
The Government has said it is “aware that there are reports of a CO2 shortage” and that the industry is “working to find a solution”.