Fizzy drinks from Cineworld, Odeon and Vue were tested in 30 cinemas as part of the Watchdog investigation.
It was found that seven branches sold drinks with unacceptable bacteria levels.
On the programme, environmental health expert Tony Lewis said he was “concerned” it was “an indicator of hygiene failure”.
Traces of the bacteria salmonella were reportedly discovered in two drinks from branches of Odeon cinemas.
Furthermore, Listeria had also been found in a drinks holder.
The claims dominated a chunk of social media discussions last night with many citing that the study had put them off buying from their cinema.
Data from the investigation tested drinks at 10 branches of Vue, Cineworld and Odean and also analysed bacteria on the seat fabric, on the cup holder and in ice cubes.
The study found that of the drinks with drinks with high bacteria levels four belonged to Cineworld, where one drink had 70 times the level considered acceptable.
Vue had one of the high bacteria drinks with Odeon having two high bacteria drinks.
Ice and drinks containing high bacteria and ingested immediately, causing concern for many health watchdogs.
Mr Lewis, head of policy at the Chartered Institute of Environmental Health, said: “That’s the highest I’ve seen. And that is an indicator of equipment not being kept clean. That’s a worry.”
Ice containing bacteria levels above an acceptable level were found in nine cinemas, Watchdog said.
Four of those ice samples were from Cineworld branches, two were from Vue, and three from Odeon.
Mr Lewis said: “Ultimately, it’s about people cutting corners And it’s also about managers, owners of cinemas, managers of cinemas, not taking their responsibilities seriously and potentially keeping on top of the issues.”
Speaking to the BBC team Odeon and Cineworld said seats, drinks holders and drink dispensers were thoroughly cleaned daily, with the ice machines emptied and fully cleaned weekly.
Odeon said it was therefore “surprised and disappointed at the Watchdog findings” and has launched an investigation of its own, adding it had “taken immediate steps” and “further strengthened procedures” across the UK.
Cineworld said the branches tested “have all been awarded the maximum food hygiene rating of five by their local authority” and its cleaning procedures were compulsory for all branches.
Vue rejected the findings, saying it “follows strict hygiene procedures daily”.