Archbishop Josiah Idowu-Fearon told the BBC Christians have not engaged in dialogue with Muslims and they feared the country was being "Islamised".
The Archbishop said that some believers had thought that Muslims leaders were supporting the militants in some cases.
The extremist group, Boko Haram, has targeted both Muslims and Christians in attacks. The organisation claims it wants to impose Islamic law in Nigeria.
It is estimated the group has killed around 10,000 people since its insurgency began in 2009.
It has also kidnapped hundreds of girls and women.
BBC Reporter John McManus says Archbishop Idowu-Fearon, who has left Nigeria to become the new secretary-general of the Anglican Communion, has a strong reputation for promoting dialogue between Christians and Muslims.
But the Archbishop said efforts needed to be made by all faiths: "We warned the leadership in my country, the Christian Association of Nigeria: 'Let us listen to the Muslim leadership, because the leadership is not in support of Boko Haram.'
"'Oh no no no,' they said, 'they are always deceiving us. They are all the same,'" he said.
He added that attitudes were changing after so many had been killed: "Now they are singing a different tune... I tell you more Muslims have been killed than Christians in the north-east of Nigeria."
* Boko Haram were founded in 2002
* The group opposes Western-style education - it translates into "Western education is forbidden"
* Joined Islamic State, now calls itself "West African province"
* Abducted hundreds, including at least 200 schoolgirls in Chibok
* Thousands killed
The Archbishop admitted his own attempts to create unity between Christians and Muslims were not always welcomed.
Mr Idowu-Fearon has also openly opposed Nigeria's laws against homosexuality, which put him at odds with many Christians in the country.
The Nigerian president Muhammadu Buhari was elected in March, partly due to his promise to defeat Boko Haram.
Since his election around 800 people have been killed by the group.
