Authorities said a gunman attacked St Philip Catholic Church early on Sunday during Mass.
Speaking to Catholic charity Aid to the Church in Need (ACN) about the attack, Bishop Hilary Paul Odili Okeke of the Diocese of Nnewi, south-east Nigeria, explained the attack was linked to local issues and not Boko Haram.
He said: "I don't think it was an attack against the Church but simply an attack that took place inside a church.
"Some people were killed immediately inside the church, while others died in hospital or in the ambulance on the way there."
While police said 11 were killed, Bishop Hilary estimates the death toll to be 13, with another 26 people injured.
On Monday the bishop visited the victims' families and also the wounded in two separate hospitals.
He said: "I met with every one of them and endeavoured to comfort them. I urged all my faithful to continue to have trust in God.
"Incidents like this can happen to any one of us and at any time, and all we can do is to leave everything in God's hands and accept his will."
According to the prelate, the church attack has caused alarm among the local community, as the mainly Christian south of Nigeria has not suffered from the terror attacks carried out in the north by Boko Haram.
He said: "There is great concern, but despite this, there were many people who came to the Mass that I celebrated yesterday in the Church of Saint Philip."
Shortly before the Mass began, a telegram of condolence arrived from Pope Francis.
The pope said he was "deeply saddened to learn of the loss of life and injury". He extended his "heartfelt condolences" to the local bishop and to "all the faithful of the diocese of Nnewi, in particular the families of the deceased and all those affected by this tragedy".
Bishop Hilary was honoured and surprised to have the pope's support.
He said: "I was surprised; I wasn't expecting to receive a message from the Holy Father. I read it out immediately to the congregation, who were extremely moved by the closeness of the Pontiff, which gave them comfort in such a tragic moment."
Now Bishop Hilary's main concern is to organise help for the wounded and for the families of the victims, and he is asking for the support of all Christians around the world.
He added: "But even more than this, we are asking our brothers and sisters in the faith to pray - for us, for the victims, and even for the attackers themselves. It is the first thing we ask of you - prayer, prayer, prayer."
No group has claimed responsibility for the attack, but the police say a manhunt has been launched.
