The Archbishops have written to Bishops in the Church of England setting out the new measures following Department of Health advice not to share "common vessels" for food or drink.
The letter said it aimed to offer guidance at a national level about how church worship could "best take into account the interests of public health during the current phase of the swine flu pandemic".
Some bishops have already taken the step in a bid to limit the spread of the virus.
For those still wishing to offer both bread and wine, the Archbishops recommended allowing the priest to dip communion wafers in the chalice before handing them out to communicants.
However presiding ministers are reminded in the letter to wash their hands thoroughly before undertaking communion.
It said: "The Department of Health have recently advised us that 'in a pandemic it makes good sense to take precautions to limit the spread of disease by not sharing common vessels for food and drink'.
"In the light of this advice, we recommend those presiding at Holy Communion suspend the administration of the chalice during this wave of pandemic flu.
"For those who still wish to offer in both kinds, we recommend the practice whereby the presiding minister, whose hands should have been washed with the appropriate alcohol based rub before handling the elements and the vessels, personally intincts all wafers before placing them in the hands of communicants."
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