Most Rev Justin Welby made the comment in an essay for the Holocaust Education Trust, which recently asked leaders in religious and public life to submit their thoughts on antisemitism for its new 'Lessons Learned?' project.
The Trust says 'Lessons Learned?' comes after an 11 percent rise in antisemitism last year, including language and imagery relating to the Holocaust where 11 millions Jews and others were murdered.
London Mayor Sadiq Khan, Secretary of State for Communities and Local Government Sajid Javed and SNP MP Angus Robertson were among those who also submitted essays to 'Lessons Learned?'.
Mr Welby said: "Antisemitism is an insidious evil... It is a shameful truth that, through its theological teachings, the church, which should have offered an antidote, compounded the spread of this virus.
"The fact that antisemitism has infected the body of the Church is something of which we as Christians must be deeply repentant.
"All humans are made in the image of God. Antisemitism undermines and distorts this truth: it is the negation of God's plan for his creation and is therefore a denial of God himself."
Rob Thompson from the Council of Christians and Jews told Premier's News Hour it is vital at a time when antisemitism in on the rise in Britain, that the Church acts in a spirit of solidarity with Jews.
He said: "This is something that has not gone away in the Church's 2000 years of history, so it's obviously a very important issue that the Church has failed to properly deal with and failed to atone for in it's theology.
"For centuries, ideas that the New Testament has superseded the Old Testament or that Jews can be blamed for Jesus' death have been preached, practised and taught in Christian churches.
"It's absolutely vital that we expose where these antisemitic ideas still exist."
Click here to hear Rob Thompson from the Council of Christians and Jews speaking with Premier's Hannah Tooley:
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