The Most Rev Justin Welby’s criticism comes as campaigners challenge ministers over the decision to accept 350 child refugees rather than the initially proposed 3,000.
They say the Government has not worked with local authorities to allocate places.
But Home Secretary Amber Rudd defended the move, arguing the scheme acted as a “pull” for people traffickers.
The archbishop admitted there was not a "simple approach" to the refugee crisis but said “leaving the whole weight of this on Italy and Greece is deeply unjust”.
The Archbishop of Canterbury called on the UK to do its part in the refugee crisis
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It's not going to stop them being trafficked, and they will end up in brothels, they will end up in places they are exploited, ill-treated, manipulated and very often finally killed
Archbishop of Canterbury Justin Welby
“These children have not chosen their way, they’re not adults, they are children,” he told BBC Radio 4’s World at One.
"Parents do not casually wake up one day and say the easiest thing to do is send our children off by themselves.”
Rev Welby warned the children fleeing to Europe were vulnerable to exploitation and even death.
He said: "This is the symptom of a situation more extreme than anything any of us can imagine and at some point the vulnerability of these children must be recognised because the alternative is they will be trafficked.
Europe in Crisis Sun, February 5, 2017
Terrorism, migrants, and crippling debt: is this the end of Europe?
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The Government has it will now accept 350 child migrants
"It's not going to stop them being trafficked, and they will end up in brothels, they will end up in places they are exploited, ill-treated, manipulated and very often finally killed."
Following the decision on Wednesday, there has been an array of criticism aimed at the Government.
Shadow home secretary Diane Abbott called the move “utterly unacceptable” while addressing the House of Commons.
She said: “How does she [Ms Rudd] live with herself? Leaving thousands of children subject to disease, people trafficking, squalor, and hopelessness.”
The Home Secretary insisted it encouraged people traffickers.
Ms Rudd said: ”I am clear that when working with my French counterparts they do not want us to indefinitely continue to accept children under the Dubs amendment because they specify, and I agree with them, that it acts as a draw.
"It acts as a pull. It encourages the people traffickers."
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