Justin Welby has been speaking to Premier in a wide ranging interview and admitted there's no simple answer to the ongoing battles within his Church.
While some claim the Church is moving away from the Bible, others claim a greater welcome needs to be given to LGBT people.
"Is there a simple answer?" he asked. "If there was a simple answer we would have found it. It is a complex of things and every church - not just the Anglicans - every church is struggling and has always struggled between the balance of what holiness looks like and how we treat those who fall short.
"Do we condemn them and expel them? Or do we only let them go on in the Church under certain conditions? Do we ignore it and say it really doesn't matter? Of course not. But the difference between setting the ideal and applying that ideal pastorally has always been a tension for the church and these issues are hugely, hugely, hugely important."
Welby called on those on both sides of the divide to work towards a better understanding of each other.
He said: "It's real people who's lives are deeply impacted and whoever it is, whatever view they take, conservative or liberal, revisionist or orthodox traditionalist, part of it - and I struggle with this, I'm not pretending I find it easy - we have to hear what they are saying.
"The trouble is sometimes people don't feel they have been heard unless they've also been agreed with, which is a bit more complicated."
Offering advice for those in the church who are confused over the issue, he gave three pointers.
"One: read the Bible carefully, not just the bits that you agree with but read it carefully and seek God's wisdom. See how Jesus treated those who thought themselves holy and those who thought themselves sinners.
"Secondly, pray a lot - particularly for those you disagree with. Not that they may be blasted or that they may be removed from the church or whatever, but that they may be blessed. Pray for them for the grace of God to fill them because they are your sisters and brothers in Christ.
"And thirdly, love one another - that's not a phrase I coined! Love one another. Jesus said to his disciples, 'Love one another as I have loved you.' Judas was one of them. He washed Judas' feet.' So they are the three things I would say pastorally and they are three things I try, not always successfully to do."
Speaking ahead of the Week of Prayer for Christian Unity, the Anglican leader was asked if it was still possible for the Church of England to stay together despite differences.
"I don't know, I genuinely don't know," he said. "What I do know is if you go to John 17 and huge passages of scripture: God is one, the church should be one to represent the oneness of God.
"We're not meant to be disunited. The reality is we are called, particularly by Jesus to be one. We are called to be one and there are only three significant problems with disunity, this is what the Bible tells us: disunity ruins our prayer life, disunity destroys our assurance of salvation in Christ, and disunity profoundly hinders our mission.
"Apart from those things, there isn't a problem with disunity! So my job is to pray for the unity of the church, to seek to help find a way for people to disagree well, within one body, and to focus on the two things we are called to do: worship God in Jesus Christ and proclaim the Gospel in deed and word.
Justin Welby also addressed criticism of recent guidance issued by the Church of England on the issue of transgenderism.
In December, a document was released encouraging church leaders to do more to make trans people feel more included.
It offered ways in which baptismal liturgy could be used to help in this way.
Clarifying its significance, he said: "This is not an instruction and there is no change of doctrine. It is simply saying [clergy can] use the structure of the baptismal liturgy to mark a transition in someone's life (not as a new baptism let's be clear, because you are only baptised once) but as a way of people affirming their identity in Christ.
"In the same way as if someone who's been baptised finds faith in Christ in a new way. Sometimes they will have a reaffirmation of their baptismal vows which will look quite like a baptism and they'll say the baptism promises and say this is who I am.
"It's guidance, it's not a rule, people are free to ignore it. And it's not a change in doctrine in any way at all."
The Archbishop of Canterbury was speaking at the launch of Thy Kingdom Come, now in its 4th year, which has united over a million Christians from more than 65 different denominations and traditions, in more than 114 countries to pray for evangelisation. It takes place between Ascension to Pentecost which this year is May 30th-June 9th.
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