Samples from drinks at Costa, Starbucks, and Caffè Nero were reportedly found to be contaminated in lab tests carried out by BBC One’s consumer series Watchdog.
Faecal coliforms, which contain disease-causing pathogens, were present in 7 out of 10 ice samples in Costa, 3 out 10 in Caffè Nero and 3 out of 10 in Starbucks, the BBC said.
Details of where the samples were collected have not been revealed.
Tony Lewis, Chartered Institute of Environmental Health, told the programme: “The level of contamination of faecal bacteria concerns me a great deal.
“The bacteria found are opportunistic pathogens - the source of human disease.
“These should not be present at any level - never mind the significant numbers found.”
Cleanliness of tables, trays, and high chairs at the chains was also tested at 30 branches.
A Starbucks spokesman said it takes hygiene ‘extremely seriously’ and ‘nothing is more important’ than customer safety.
“We have moved quickly to conduct our own investigation into the claims about the stores,” he added.
“All employees nationwide have received updated training on our high standards of hygiene including ice handling.”
Costa said: “We were disappointed with the findings, especially as these stores are all rated ‘very good’ with a the top hygiene rating of five.
“Following these results we took immediate action to review our food safety procedures and have updated our ice-handling guidelines and are in the process of introducing new ice equipment storage across our estate.”
A spokesman for Caffè Nero described the findings as concerning and added: “A thorough investigation is now under way and the appropriate action will be taken.”
“99 per cent of our stores are rated as very good, good or satisfactory by their local environmental health officer - making us one of the most highly rated businesses on the high street,” he said.
The first episode of the new Watchdog programme will air on BBC One tonight at 8pm.