Calm has reportedly returned to the affected region after a heavy military crackdown in which several members of the Boko Haram movement, including the leader Mohammed Yusuf, were killed.
A statement signed by Fr Louis Odudu, Deputy Secretary-General of the Catholic Secretariat of Nigeria, reminded Boko Haram of the need for tolerance.
"We, therefore, call on the leaders of the Boko Haram movement (translated as Western education is sin), currently causing hardship for innocent ordinary citizens in the northern parts of the country, to adopt a creative approach to their religious practice in order to give honour and glory to Almighty God."
The church said that the underlying pillars of any religion include the principles of justice and progress; tolerance and the dignity of all human beings.
"Modern education and modern civilizations do not preclude ardent religious devotion. In fact, it should be underlined that Islam, as a religious practice, from places like Al-Azhar, carried the light of learning through so many centuries and paved the way for Europe's renaissance and enlightenment."
Muslim communities have contributed to the development of the order of algebra, magnetic compass and tools for navigation, the mastery of pens and printing, mastery of the knowledge of diseases and healing technologies, timeless poetry and cherished music, and calligraphy, the church stated.
"We therefore condemn any religious movement that would subvert the progress that has been made in education and technology in Nigeria and at the same time thwart law and order. We condemn a descent to religious fanaticism that would destroy our national peace and stability."
The church also accused Nigerian government of condoning the growth of the Boko Haram movement and called for urgent efforts to control the upsurge of religious militancy in the country.
The government should also ensure that the perpetrators of the violence face the full weight of the law.
The church attributed the cause of the Boko Haram uprising and other forms of violence to widespread poverty and urged the government to urgently address the problem.
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