The Church said it had "significant concerns" about the presence of the secretive organisation after more than ten Anglican cathedrals hosted special services for Masonic lodges.
The United Grand Lodge of England (UGLE), which has more than 200,000 members, marked its 300th anniversary last year.
Speaking at the Church's General Synod meeting, the Bishop of Coventry flagged up a 1987 report issued by the church that highlighted a "number of very fundamental reasons to question the compatibility of Freemasonry and Christianity".
The Rt Rev Dr Christopher Cocksworth responded to a question tabled on the second day of the three-day meeting in London of the Church's governing body.
Canterbury, Winchester, Salisbury, Manchester, Truro, Wells, Lincoln, Exeter, Chester, Leicester and Peterborough cathedrals all hosted Freemasons in 2017.
According to West Kent Masons, the Canterbury service last February was prepared in conjunction with the Very Rev Dr Robert Willis, the dean of Canterbury Cathedral, who also delivered the sermon.
Lambeth Palace confirmed that the Archbishop of Canterbury was not, and had never been, a Freemason.
His predecessor, Rowan Williams said Christianity and Freemasonry were "incompatible" and refused to appoint clergymen to senior posts if they were known to be members of the group.
However, in 2011 he sparked controversy after appointing a known senior mason as the Bishop of Ebbsfleet.
Meanwhile, the Freemasons' leader said on Friday that the organisation have been "undeservedly stigmatised", and will be running a series of open evenings to prove it is not a secret society.
The United Grand Lodge of England placed adverts in three national newspapers headlined "enough is enough", saying it is the victim of misrepresentation.
Chief executive Dr David Staples said he had written to the Equality and Human Rights Commission about concerns its members are the victims of gross misrepresentation and discrimination.
He said: "Our members shouldn't have to feel undeservedly stigmatised.
"No other organisation would stand for this and nor should we.
"I appreciate that you may have questions about who we are and what we do, so why not ask those who know?"
Last year, the United Grand Lodge of England raised more than £33 million for good causes, he added.
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