The shooting at Emanuel AME Church last Wednesday, seen as a racist attack, has sent shockwaves through southern states and re-stoked the national debate about race relations in America. But after the initial outpouring of grief and the inspirational offers of forgiveness from the victims' relatives, the wider Church is also choosing this moment to reflect on systemic issues that may be affecting race relations.

Amid calls for the Confederate flag to be removed from state buildings and car licence plates, numerous American Christian leaders have called for the Church to acknowledge and repent of its historical role in the oppression of black people.

The motives of the suspected killer, Dylann Roof, are not fully known, but one survivor reported that the shooter said: "I have to do it. You rape our women. You're taking over our country. You have to go." Roof's friends have said he condoned racial segregation and wanted to start "a civil war". Last weekend a website was found with a 'manifesto', widely attributed to Roof, which seems to suggest a racial motivation for the attack.

Charleston is a deeply symbolic location for a racist attack as it was a key port town for Africans brought to America as slaves. Emanuel Church is the oldest black congregation south of Baltimore; one of the church's founders, Denmark Vesey, began organising a major slave uprising in Charleston in 1821, though the plot was foiled before the uprising took place and he was hanged for his crime.

It is one of the ugly truths of Christian history that biblical texts were often used to justify the slave trade, particularly in the southern states in the 19^th century where slavery was big business. Perhaps the most famous biblical text used is the passage in Genesis 9:20-27 known as the 'curse of Ham' which tells the story of Noah and his three sons. When Noah got drunk, Ham saw him lying naked in his tent and ran to tell his brothers. For this, Noah curses Ham and says "The lowest of slaves will he be to his brothers."

Professor Stephen Haynes, who teaches on racism and religion at Rhodes College, Tennessee, told Christian Today that although most Christians now would suggest it was "sort of ridiculous" to see this as condoning slavery, it was seen as a key text at the time.

Christians also looked to the passages in the New Testament which spoke of slaves honouring their masters, and said that it was further proof the Bible supported the slave trade. They pointed to passages such as Ephesians 6:5, where Paul writes: "Slaves, obey your earthly masters with respect and fear, and with sincerity of heart, just as you would obey Christ." There are similar instructions given in Titus 2:9 and 1 Peter 2:18. Most theologians would now interpret these as being about slaves honouring God in their current situation (essentially, making the best of a bad job), but Haynes says: "The motto that a lot of Southern Christians would have used [at the time] was 'slavery was instituted in the Old Testament and assumed in the New'."

While it is widely recognised that the Bible has been used to support slavery, Haynes' recent academic work has looked at the less-discussed biblical arguments used by Christians who were arguing for segregation in the 1950s and 60s. He points out that many looked again to Genesis 9-11 for justification, this time referring to God's plan to disperse humanity to demonstrate that God didn't expect people to congregate together. Though he says there is the occasional segregationist group which uses these same verses today, such views are far from being widespread.

Many would say that this history has already been dealt with. The Southern Baptist Convention, for example, issued its resolution on racial reconciliation repenting of its past in 1995. "What most white Christians, and most white Americans, have wanted to do is hit the reset button on American history," Haynes says. "They have wanted to say things in the past were bad, there was racism in the past but things are better now – there's equality of opportunity so let's just move forward.

"There was never a truth and reconciliation process in this country after the civil rights movement," he says, adding: "I think Churches need to take the lead in revisiting this. We have never really acknowledged our own role, our own complicity in this. We need to take the time to make that clear."

This is a common sentiment. Since the Charleston shooting, many theologians and church leaders have said that historical repentance was not enough. Rev Dr Susan Brooks Thistlethwaite, professor of theology at Chicago Theological Seminary, wrote in the Huffington Post last week that the Church should clearly declare that "white supremacy is a heresy". Rev Al Mohler, president of the Southern Baptist Theological Seminary in Louisville, Kentucky, wrote in Baptist Press about the "putrid exegesis" of biblical texts which has been used to justify the heresy of racial superiority.

Haynes suggests that this marks a pivotal moment. "Christians... of all stripes, are on the same page about this incident – it has to be condemned, and that if there's anything that's holding back race relations, it needs to be sacrificed."

Sacrifices are already being made. On Tuesday the South Carolina legislature voted overwhelmingly to remove the Confederate flag from the State House, followed by numerous calls to remove it from public sites in other southern states, including the proposal from Mississippi House Speaker Philip Gunn to change their state flag – the state voted to keep the symbol of the Confederacy on their flag in 2001. Gunn, who is also a leader in his Baptist church, said in his statement that his Christian views had influenced his decision. Mississippi Attorney General Jim Hood voiced his support for Gunn's suggestion, saying that he had asked himself "What would Jesus do?"

Russell Moore, president of the Southern Baptist Ethics and Religious Liberty Commission, who is from Mississippi, is among the religious leaders calling for the removal of the Confederate flag. Last Friday he wrote a blog saying: "White Christians ought to think about what that flag says to our African-American brothers and sisters in Christ, especially in the aftermath of yet another act of white supremacist terrorism against them."

Christian civil rights lawyer Joshua Rogers agrees. "What are you really holding onto when you refuse to let go of that flag?" he wrote in a blog. "At what point in your Christian life did you become convinced that holding onto a strip of cloth was worth alienating your own family members in Christ?"

Haynes sees Moore's stance, and other religious conservatives who agree with him, as an interesting development – describing it as "speaking in ways that one would have thought of as very liberal in the past; that is, taking history and its legacy very seriously".

But even before Charleston there were calls for change for a renewed focus on race among Christians. Earlier this month, two scholars from the Presbyterian Church in America put forward a 'personal resolution on civil rights remembrance' for consideration by the PCA's general assembly. In the statement Dr Sean Lucas and Dr Ligon Duncan say that they "recognize and confess our church's covenantal and generational involvement in and complicity with racial injustice inside and outside of our churches during the Civil Rights period". They also say that the Church's failure to speak out against this has hindered "present-day efforts for reconciliation with our African American brothers and sisters". After some discussion at this year's general assembly, it was referred to next year's meeting for further debate.

Charleston is hardly the first incident this year which has called American race relations into question. The deaths of Eric Garner in July and Michael Brown in August last year, the subsequent protests in Ferguson and in then in Baltimore in April, have all demonstrated that racial inequality is still a live issue, and therefore an issue for the Church.

Some initial coverage of Charleston suggested that it was an attack on Christianity. While this idea has been widely derided for shifting the debate away from race, Haynes suggests that the fact that the event took place in a church may have encouraged the strong stance from Christian leaders: "The circumstances were so demonic that it just really made people realise, that whatever was motivating this guy was deeply unchristian, and deeply evil."

While the idea that an act of racial hatred had to take place in a church to provoke this response is an uncomfortable one, there are numerous factors which seem to have shifted in order to produce the swelling shift in opinion – creating, perhaps, a unique moment for white Christians in America both to revisit their past and look at their present, and to ensure that this time they do stand up and fight for justice.