US President Barack Obama has denounced the killing of nine people in a Charleston, South Carolina church, saying death happening in a place of worship is "heartbreaking."

The shooting—carried out by a 21-year-old white gunman identified as Dylann Roof who was subsequently arrested after the shooting—is deemed by a security expert as the worst attack on a congregation in American history. The victims, the oldest of whom was 87 and the youngest at 26, included Rev. Clementa Pinckney, a senior pastor of the church.

"Any death of this sort is a tragedy. Any shooting involving multiple victims is a tragedy. There is something particularly heartbreaking about the death happening in a place in which we seek solace and we seek peace, in a place of worship," Obama said in a briefing on Thursday.

Obama said he and the First Lady personally knew the pastor slain in what has been called a "hate crime."

"Michelle and I know several members of Emanuel AME Church. We knew their pastor, Reverend Clementa Pinckney, who, along with eight others, gathered in prayer and fellowship and was murdered last night. And to say our thoughts and prayers are with them and their families, and their community doesn't say enough to convey the heartache and the sadness and the anger that we feel."

Obama emphasised that the attack, which is a reminder of a "dark part" of US history, was not the first of its kind.

"The fact that this took place in a black church obviously also raises questions about a dark part of our history. This is not the first time that black churches have been attacked. And we know that hatred across races and faiths pose a particular threat to our democracy and our ideals."

"Mother Emanuel is, in fact, more than a church. This is a place of worship that was founded by African Americans seeking liberty. This is a church that was burned to the ground because its worshippers worked to end slavery. "

Carl Chinn, a security expert, said he has recorded more than a thousand attacks on places of worship since 1999.

This year, there have been over 150 so far, and the recent attack on the pastor and parishioners of Emanuel African Methodist Episcopal Church, according to Chinn, was the worst church attack in American history, Fox News reported.

"This was a calculated attack," Chinn said. "It's just awful. I hurt for those people."

More worrisome, the attack may just be the beginning for more in the future, according to Tim Miller, one of the country's top experts on church security.

"Violence directed against the church has been growing over the past decade," said Miller, who heads the LionHeart International Services Group. "My fear is what we saw in Charleston is one incident of many more to come."

Catholic bishops on Thursday deplored the killing of the Methodist pastor and his parishioners inside the sacred halls of the historic African-American church, the Catholic News Agency reported.

"The inside of any church is a sanctuary. When a person enters, he or she has the right to worship, pray and learn in a safe and secure environment," Bishop Robert Guglielmone of Charleston said. "For anyone to murder nine individuals is upsetting, but to kill them inside of a church during a Bible study class is devastating to any faith community."

"I pray that everyone affected by this horror will feel the comforting presence of our Lord surrounding them during this difficult time," he added.

"We pray for those killed in the violent church shooting in Charleston. We also pray for their families and all those who mourn their death," Bishop Michael Burbidge of Raleigh posted on Twitter.