At least one bishop also urged the government to dialogue with the leadership of the Movement for the Emancipation of the Niger Delta, which has been linked to attacks on petroleum installations in southern Nigeria.
"Churches in northern Nigeria and my diocese in particular have been recording depletion in the number of faithful attending church services owing to Boko Haram insurgencies there in recent years,'' said Bishop Stephen Dami Mamza of Yola. He said many Christians had moved to other parts of the country.
Mamza told Catholic News Service that many residents in northern Nigeria and especially in Yola now live in fear that Boko Haram could strike at any time, killing innocent people.
"We religious leaders are assuring them that their security is in the hands of God and (they) should not abandon God's house," he said.
In early April, the Nigerian government set up a technical committee to advise President Goodluck Jonathan on whether to grant amnesty to Boko Haram, an Islamist sect blamed for the deaths of at least 1,400 people since 2010. The committee, whose members included security chiefs and ministers who form the security council, submitted its report to Jonathan April 16 in Abuja.
The bishops who spoke to CNS were in Iseyin to mark the golden jubilee of the erection of the Catholic diocese of Oyo, in which Iseyin is located, and to celebrate the priestly ordination of six seminarians.
Archbishop Felix Alaba Job of Ibadan, referring to Boko Haram's targeting of civilians, questioned why the government should "grant amnesty to vandals of human souls and bodies."
Retired Bishop Julius Babatunde Adelakun of Oyo said granting amnesty to Boko Haram was "like granting amnesty to terrorists, it is unthinkable."
Adelakun alleged that government leaders in northern Nigeria know Boko Haram members and should become more involved in initiating dialogue and reconciliation. He said Nigerians should continue to pray that God "grant them a change of hearts, that is what they need."
Bishop Felix Femi Ajakaye of Ekiti said if the government grants amnesty to Boko Haram, other groups would ask for amnesty, too.
"And when you go on granting amnesty to this sect, what about the victims of the Boko Haram's insurgency?'' he asked.
Such favour from the Nigerian government could amount to supporting injustice, which Nigerians and their leaders must discourage, he added.
He said suspects arrested in connection with Boko Haram's bombing cases should be prosecuted to serve as a deterrent to others. He noted that Kabiru Sokoto, the Boko Haram leader alleged to have masterminded the Christmas bombing of St. Theresa Catholic Church in Madalla, has not been prosecuted.
Ajakaye also urged the Nigerian government to dialogue with the leadership of the Movement for the Emancipation of the Niger Delta about the need to build on the peace the southern part of the nation is currently enjoying.
The movement's officials threatened to resume destruction of crude oil installations in the Niger Delta following the jailing of their leader, Henry Okah, by a South African court.
"It is a minus to Nigeria that Okah should be sentenced in South Africa, but those that were arrested by the security agencies in Nigeria" who were linked to Okah's activity have not been prosecuted, Ajakaye said.