Fizzy drinks from Cineworld, Odeon and Vue were tested in 30 cinemas, for BBC One's Watchdog programme.
Seven branches sold drinks with unacceptable bacteria levels.
Environmental health expert Tony Lewis said he was "concerned" it was "an indicator of hygiene failure".
Traces of the bacteria salmonella, which can cause food poisoning, were reportedly discovered in two drinks from branches of Odeon cinemas. Listeria had also been found, in a drinks holder, Watchdog said.
'10,000 times higher'
The investigation tested drinks at 10 branches of each company. It also looked for bacteria on the seat fabric, on the cup holder and in ice cubes.
The results were sent to London Metropolitan University's "superlab" to be tested.
According to Watchdog, out of the seven cinemas 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, and this was 100 times the acceptable level
- Odeon had two high bacteria drinks and one had 10,000 times the acceptable level
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."
Watchdog reported mixed results on bacteria on the seats and in drinks holders. Since those bacteria are unlikely to reach your mouth, they are thought to be less of a concern.
The cinema chains have all told the programme they take hygiene "incredibly seriously" and have robust cleaning procedures in place.
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 had immediately launched its own investigation, 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".
It also said it undertook its own independent tests regularly, "conducted by a qualified clinical microbiologist with nationally recognised accredited training", and worked with "third-party water experts, exceeding the requirements for water testing".
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