Some schools have already stopped using the tubes, made famous by the Blue Peter programme along with washing-up liquid bottles, and the latest health advice backs them up.
Writing in the British Medical Journal, Dr Ian Hosein, consultant microbiologist at the Public Health Laboratory Service, warns: "Because of the potential for rapid spread of enteric [intestinal] diseases in nursery and infant schoolchildren I think that the cardboard tubes should not be used. "
He said the tubes could be soiled by people using the toilet before they have washed their hands.
Wendy Scott, chair of the British Association for Early Years Education, said: "There are many alternatives such as the tubes from kitchen rolls and aluminium foil which are stronger and more useful because they come in different lengths."
A BBC spokesman said Blue Peter presenters now only recommend using kitchen roll tubes.