Thousands of them have been supplied to clergy around the country after reports of parishioners suffering from coeliac disease being laid low with digestive problems.
Gluten is a protein found in wheat - one of the main ingredients of the holy bread used in the celebration of the Eucharist.
For centuries, the plight of church-goers suffering from the potentially fatal condition had been largely ignored.
But now, greater public awareness of health issues has forced the church to make special provision for communicants who fear that placing a normal wafer on their tongue could set off an allergic reaction.
The gluten-free wafers are square so that they can easily be differentiated from the normal round ones.
Charles Farris, a leading supplier of ecclesiastical products, sold 4,000 boxes of 50 last year and says demand is strong, despite a marked difference in price.
Because the gluten-free version requires a more complicated manufacturing process, each wafer sells for about 9p - four times as much as a standard one.
At Christ Church Cathedral, Oxford, where gluten-free wafers are kept on a separate plate on the altar rail, diocesan spokesman Sarah Meyrick said: "This is particularly important for us as we have a large number of visitors.
"We make an announcement about the gluten-free wafers at services where congregations are bigger than normal, for example at Christmas, Easter and ordinations.
"Both types of wafer are consecrated together at the central altar, along with the communion wine.
"We know about the needs of regular attenders but this system ensures that we are not caught out if someone turns up out of the blue and makes a similar request."
In the Roman Catholic Church, the issue has doctrinal implications and five years ago was the subject of an edict from Joseph Ratzinger, the German cardinal who became Pope Benedict XVI in 2005.
He ruled that bread used at Holy Communion must contain at least a tiny amount of gluten in order for it to be "valid matter for the celebration of the Eucharist".
As a result, wafer manufacturers supplying Catholic churches have developed a product with a gluten content so small that coeliacs can eat it without any ill effects.
Coeliac disease is a lifelong auto-immune condition for which there is no known cure.
Research suggests that in Britain one person in 100 suffers from it.
Lack of treatment can lead to anaemia, osteoporosis and an increased risk of bowel cancer.
Everyday foods such as bread and pasta damage the lining of the gut but most symptoms disappear once the patient embarks on a gluten-free diet.
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