Cardinal John Onaiyekan, Archbishop of Abuja, believes the majority of fighters have been forced to join the terror group and do not share its Islamist ideology.
According to the Catholic Diocese of Maiduguri, in Boko Haram's prime target area of north-east Nigeria, at least 5,000 faithful have been killed, with 350 churches and presbyteries destroyed, while up 100,000 people were displaced.
"More people are in Boko Haram because they were drafted and had no choice," said Archbishop Onaiyekan to Catholic charity Aid to the Church in Need.
"Those who would espouse the theology of Boko Haram are not that many. It means that of those up to 70 or 80 per cent will want to come out, " added the archbishop.
The cardinal admitted a policy of offering asylum to Boko Haram soldiers was not popular with many Christians.
"There should be a commitment. If they come out, you will treat them well. That will encourage more to come out.
"But if you treat them badly and slaughter them, that will stop others from coming out.
"Our country is big enough and strong enough to take the risk of amnesty."
He said: "Boko Haram succeeded in destroying all goodwill between Muslims and Christians in those areas where [the terror group] was active.
"In some cases we have seen a lot of anger between Muslims and Christians.
"A lot will need to be done to recover, to enable them to work together."
Recent reports have suggested Government forces has made breakthroughs in the struggle against the terror group, with against Boko Haram in the groups traditional heartland in the north-east, but the terror group's leader Abubakar Shekaku dismissed the claims as "lies".
Archbishop Onaiyekan praised President Buhari's initiatives to form a coalition against Boko Haram, collaborating with neighbouring Chad, Cameroon and Niger.
Cardinal Onaiyekan said: "In the past month we have seen evidence of major inroads into the areas of Boko Haram.
"It can be said that today they no longer control large sections of our national boundary. They no longer hold areas that are out of bounds to everybody but them. But they are still around and can create havoc."
While praising the policies of new Nigerian President Mohammadu Buhari in tackling Boko Haram since he took office in May, the cardinal said successes had also against the terror group has been achieved by of Christian President Goodluck Jonathan.
He also praised President Buhari's initiatives to form a coalition against Boko Haram, collaborating with neighbouring Chad, Cameroon and Niger.
The Cardinal said further negotiations by the new President had brokered with leading powers such as France and the US including the sharing of intelligence.
