Most Revd Dr Josiah Atkins Idowu-Fearon, the current Bishop of Kaduna, is to take on the role which reaches out to Anglican churches across the world.
But since his appointment some have accused him of being anti-gay.
It's claimed in March 2014 he told the Nigerian newspaper New Telegraph: "Our battle today is not against homosexuals, our battle today is against those who say God's standards are not good enough for us.
"The government has criminalised homosexuality which is good, our battle is not against human beings, it is against the devil."
Both male and female same-sex sexual activity is illegal in Nigeria.
In 2007 he told the Dallas Morning News on gay people: "I feel we are deceived, we have been cheated by the people the Lord Jesus Christ used to introduce us to the Scriptures, to bring us to a new faith in the Lord Jesus.
"They are telling us that it's not wrong after all, that it's a natural way. But we say: You are wrong; the Bible is right.
"So it's not just a question of human sexuality. It's about the authority of Scripture. For us, Scripture judges every culture. What I hear in the Western world is that culture judges Scripture. That's the basic difference. It's not a question of sex or no sex."
But in a letter posted on the Facebook group Episcopal Women's Caucus he said: "I do not support the law in my country that criminalises homosexuality".
He added: "That has been my position and it has not changed. The church must always critique any government policy that is discriminatory, that is why the church is there!
"When any government enacts or passes any law that is wrong, the church must and should provide an alternative.
"I hope my clear and unapologetic position will make it possible for us of the same Anglican Family to talk with rather than at each other.
"I have spent over 40 years working on the culture of respect for differences among Christians and Muslims in Nigeria and Africa, this is what I believe the Lord has called me to spend the rest of my life and ministry doing now within our own Family: the Communion."