The Right Rev David Walker also raised concerns that people with gluten allergies can be affected by the tradition.
"We are becoming increasingly aware of the severe reaction some people have to gluten," Bishop David told The Times.
"As a result churches are now used to providing gluten-free bread in services of Holy Communion. However, what is often overlooked is that dipping wafers in the wine can introduce gluten, which others then drink."
Many Church of England parishes take part in the practice where the wafer, representing the body of Jesus Christ, is dipped into wine, which represents Christ's blood.
Many churches have already stopped dipping wafers into wine with others encouraging people concerned about catching or passing on infections to abstain from joining in with communion.
The tradition of asking worshippers to shake hands and "exchange the peace" has also regularly been stopped during outbreaks of flu.
Bishop David added: "It is already advised nationally that, for reasons of hygiene, the intinction of wafers should be avoided.
"When a wafer is given into the hands of a communicant it may become contaminated by germs lying on the skin. Intincting the wafer then introduces those germs directly into the wine.
"There is also the possibility of finger tips inadvertently dipping into the liquid."
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