Justin Welby told the BBC's 'Songs Of Praise' show the killings had put a "chink in his armour".
"Saturday morning, I was out and as I was walking I was praying and saying,'God, why - why is this happening? Where are you in all this?' and then engaging and talking to God. Yes, I doubt," the archbishop said.
He said the shock he felt over the incident was "added to because my wife and I lived in Paris for five years."
A bombing campaign against ISIS, particularly by French air forces, was launched in Syria shortly after the attack, but the archbishop warned against a potentially damaging instant reaction.
"Two injustices do not make justice. If we start randomly killing those who have not done wrong, that is not going to provide solutions. So governments have to be the means of justice," he said.
They will discuss how to cooperate on counter-terrorism and in the fight against IS in Syria and Iraq.
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