Brewers and soft drink manufacturers use CO2 for carbonation - making drinks fizzy.
Ethanol producers capture CO2 as a byproduct and sell it to the food industry in large quantities.
But ethanol production - which is blended into the nation's fuel supply - has fallen sharply due to the drop in petrol demand as a result of lockdown measures during the coronavirus pandemic.
Petrol demand is down by more than 30% in the US, and the dwindling ethanol output is affecting the food industry as a result.
And CO2 suppliers have increased prices by around 25% due to reduced supply, according to Brewers Association chief executive Bob Pease.
The trade group represents small and independent US craft brewers, who get about 45% of their CO2 from ethanol producers.
Mr Pease added: "The problem is accelerating. Every day we're hearing from more of our members about this."
He expects brewers will start cutting production in two to three weeks.
In a letter to Vice President Mike Pence on 7 April, the Compressed Gas Association (CGA) said production of CO2 had fallen by about 20%.
It added that it could be down by 50% by mid-April without relief.
Meat producers are also being affected as they use CO2 in processing, packaging, preservation and shipment.
