The Most Rev Justin Welby said that there had been more than 80 Christian “martyrs” in the last few days alone.
He was speaking about the bombing of All Saints Anglican church in Peshawar, Pakistan, in which 85 were killed and more than 200 injured.
Christian communities which have existed “in many cases since the days of Saint Paul” are now under threat in countries such as Syria and Egypt, he said.
Last month around 100 Christian sites were attacked amid the turmoil in Egypt, with 42 churches burnt to the ground. Ancient Christian communities in Syria have also been singled out for violence.
But speaking during an interview on BBC Radio 4, Archbishop Welby, who leads almost 80 million Anglicans around the world, said it was the duty of Christians to pray for their killers.
He said that in many cases apparently religious conflicts are actually bound up with other social and historical grievances but that this could not explain several recent attacks on Christian.
“The appearance is often deceptive but I think Christians have been attacked in some cases simply because of their faith,” he said.
“I think it is true to say – and also in Peshawar – that we have seen more than 80 martyrs in the last few days.
“They have been attacked because they were testifying to their faith in Jesus Christ by going to church.
“That is outside any acceptable expression in any circumstances for any reason of religious difference.”
He said the Church had been raising its fears for Christians abroad with the Foreign Secretary William Hague and called on other Governments to act to protect them
But he added: “As Christians one of the things is that we pray for justice and particularly the issues around the anger that comes from his kind of killing.
“But we are also called as Jesus did at the cross to pray for those who are doing us harm.”
He also emphasized that the Muslim religious leaders in Britain and overseas had been as appalled at the attacks on Christians as he was.