A white man walked into a historic African-American church in Charleston, South Carolina, and opened fire during a Bible study class, killing nine people Wednesday evening.

Eight died at the scene; a ninth at a hospital, police said. Among them is the church's pastor, the Rev Clementa Pinckney.

The shooting at the Emanuel African Methodist Episcopal Church, the oldest AME church in the South, is being investigated as a hate crime.

"The only reason someone would walk into a church and shoot people that were praying is hate," said Charleston Mayor Joe Riley.

The suspect, Dylann Roof, 21, of Lexington, South Carolina, was arrested Thursday morning about 245 miles (395 kilometres) away in Shelby, North Carolina, law enforcement authorities said.

He was taken into custody without incident about 11:15 am during a traffic stop, Charleston police Chief Greg Mullen said. Local police were acting on a BOLO (be-on-the-lookout) notice that included a vehicle description, the licence tag and the suspect's name.

Roof was armed with a gun when he was arrested, according to a law enforcement official briefed on the investigation. It's not clear if it's the same firearm used in the shooting.

A senior law enforcement source told CNN the suspect's father had recently bought him a .45-caliber gun for his 21st birthday in April.

President Barack Obama mourned the violence and the victims, saying, "Any death of this sort is a tragedy. Any shooting involving multiple victims is a tragedy. There is something particularly heartbreaking about death happening in a place in which we seek solace, we seek peace."

Sylvia Johnson, a cousin of Pinckney, said she heard about what happened inside the church from survivors.

Johnson said survivors recounted the man coming into the church, asking for Pinckney and sitting next to him during a prayer meeting for an hour. He started shooting and reloaded five times, she said.

When a man pleaded with him to stop, the shooter replied, "You rape our women and you're taking over our country. And you have to go," she said.

A law enforcement official says witnesses told authorities the gunman stood up and said he was there "to shoot black people."

Police were searching for more information about Roof (whose last name is rhymes with "cough"), and trying to determine if he had any links to hate groups.

HISTORIC SIGNIFICANCE

The Emanuel African Methodist Episcopal Church has been a presence in Charleston since 1816, when African-American members of Charleston's Methodist Episcopal Church formed their own congregation after a dispute over burial grounds.

It was burned to the ground at one point, but rebuilt. Throughout its history, it overcame obstacle after obstacle -- destroyed by an earthquake, banned by the state. But its church members persevered, making it the largest African-American church in terms of seating space in Charleston today.

Every Wednesday evening, the church holds a Bible study in its basement.

The shooting was "obviously the most intolerable and unbelievable act possible," the mayor said.

"People in prayer Wednesday evening. A ritual, a coming together, praying, worshiping God. An awful person comes in and shoots them is inexplicable," Riley said.

Police received the first call around 9:05pm. Officers arrived to find several victims inside.

"It's really bad. It's a very bad scene," local pastor Thomas Dixon said.

Worshippers comfort each other across the street from a historic African-American church in Charleston, South Carolina, where a white man walked into and shot dead nine during a Bible class on Wednesday night. Police believe the attack is a hate crime. Photo: AP

'SICK TO OUR STOMACHS'

The church sits in an area of Charleston densely packed with houses of worship and well-preserved old buildings.

The city, as several church leaders pointed out, is known as the "Holy City" for its tolerant attitude toward different denominations.

It was led by Pinckney, who was also a state senator. His death was reported by affiliate WCSC, who confirmed it through Elder James Johnson, the president of the Tri-County chapter of the civil rights organization the National Action Network.

Recently, Pinckney backed a bill to make body cameras mandatory for all police officers in South Carolina. The legislation was in response to the death of Walter Scott, an unarmed black man killed by a police officer earlier this year.

"Body cameras help to record what happens. It may not be the golden ticket, the golden egg, the end-all-fix-all, but it helps to paint a picture of what happens during a police stop," Pinckney said in April.

Early Thursday morning, residents stood in circles, hands clasped and heads bowed, as they prayed.

"Like everybody out here, we're sick to our stomachs that this could happen in a church," Rep. Dave Mack, a friend of the church's pastor, said.

They called for justice, but also for calm. Theirs is a strong community, they said, and this incident wouldn't tear them apart.

The head of the NAACP expressed his outrage over the shooting.

"There is no greater coward than a criminal who enters a house of God and slaughters innocent people engaged in the study of scripture," Cornell William Brooks said.

Republican presidential candidate Jeb Bush cancelled a scheduled town hall in Charleston on Thursday because of the shooting.

"As the #Charleston police deem this horrific act a hate crime," the King Center tweeted, "we pray vigorously that this person's hate does not cultivate more hate."