Samples of iced drinks from Costa Coffee, Starbucks and Caffe Nero contained varying levels of the bacteria, the BBC’s Watchdog found.
Expert Tony Lewis said the levels found were “concerning”.
“These should not be present at any level – never mind the significant numbers found,” he added.
Cleanliness of tables, trays, and high chairs at the chains was also tested at 30 branches.
Seven out of 10 samples of Costa ice were found to be contaminated with bacteria found in faeces.
At both Starbucks and Caffe Nero, three out of 10 samples tested contained the bacteria known as faecal coliforms.
Mr Lewis, of the Chartered Institute of Environmental Health, said these kinds of bacteria were “opportunistic pathogens – the source of human disease.”
All three chains affected said they had now taken action.
Costa said it had updated its ice-handling guidelines and was in the process of introducing new ice equipment storage…