Speaking to ABC News, the US president said while Islamic State beheads Christians in the Middle East and America continues to ban torture, "we're not playing on an even playing field."
Trump told interviewer David Muir: "When they're chopping off the heads of our people and other people. When they're chopping off the heads of people because they happen to be a Christian in the Middle East, when ISIS is doing things that nobody has ever heard of since medieval times, would I feel strongly about waterboarding?
"As far as I'm concerned, we have to fight fire with fire."
Trump said he had spoken with people at "the highest level of intelligence" and they told him that waterboarding - a form of torture - is effective.
"I asked them the question does waterboarding work? And the answer was yes, absolutely," he said.
But Trump's comments were slammed by a number of Christian leaders.
Speaking on Premier News Hour, Canon Mark Soady, a campaigner against torture methods, said it's an outrageous suggestion.
"It's wrong morally because we would be as bad as those who do the terrorists acts if we behave in this uncivilised and barbaric way. All studies into waterboarding and similar tortures have shown that they are not effective."
He added that it is the duty of Christians to forgive those that hurt them.
"We are all created in the image of God and we need to treat our fellow human beings as if they were God," he said, "Christ teaches us that we must forgive and go on forgiving. That means we must not use the same methods that our enemies use."
Founder of Oasis Church and anti-slavery charity Stop the Traffik Steve Chalke tweeted: 'As Jesus taught, somewhere in here I'm sure, bring on the torture, fight fire with fire'."
'As Jesus taught, somewhere in here I'm sure, bring on the torture, fight fire with fire' pic.twitter.com/LBesDa9Xy9
— Steve Chalke (@SteveChalke) January 26, 2017
And Brian Zahnd, pastor of World Life Church, tweeted: "Once you try to reconcile 'love your enemy' with 'torture works', you know you've forsaken Christ and are only pretending to be Christian.
Once you try to reconcile "love your enemy" with "torture works," you know you've forsaken Christ and are only pretending to be Christian.
— Brian Zahnd (@BrianZahnd) January 26, 2017
The interview was aired yesterday, the same day that Trump signed an executive order to begin construction of a US-Mexican boarder wall.
Listen to Premier's Aaron James speaking to Canon Mark Soady here: