Producer Warbutons said it is working "really hard" to keep products on shelves, but admitted it is making "nowhere near" its usual amount of the British staple.
Just one of its plants - at Eastwood in Nottinghamshire - has been operating normally, it said.
Two others - in Enfield, north London, and Burnley, Lancashire - are not producing any goods, while its Stockton-on-Tees branch has received a small supply of CO2 after being offline for days.
Tearmh Taylor, corporate and consumer affairs manager at Warburtons, said: "As a result of the ongoing CO2 shortage, we are producing nowhere near the 1.5 million packs of crumpets we usually make each week and have had to suspend production at a number of our bakeries.
"This will remain the case until the CO2 supply returns to normal, but rest assured we are working really hard to keep our products on Britain's shelves."
The shortages are understood to have been caused by a longer than usual break in production of ammonia, one of the key sources of food grade CO2 in Europe - which is used to carbonate drinks and preserve some packed fresh foods.
Trade journal Gas World said the shortage had been described as the "worst supply situation to hit the European carbon dioxide (CO2) business in decades".
A spokeswoman for the British Retail Consortium (BRC) said CO2 supply issues remained and it was likely the "mix of products available may be affected".
It comes as some pub chains reported they had temporarily run out or were short of John Smith's, Strongbow, Amstel and Birra Moretti as disruption to supplies of CO2 began to take effect at the bar.
The British Beer and Pub Association (BBPA) said stocks of the gas remained low but brewers were "working their socks" off to ensure the beer continued to flow.