Police lead suspected shooter Dylann Roof into the courthouse in Shelby, North Carolina, June 18, 2015. [Photo/Agencies]

CHARLESTON - A white man was arrested on Thursday on suspicions he killed nine people at a historic African-American church in South Carolina after sitting with them for an hour of Bible study in an attack US officials are investigating as a hate crime.

The mass shooting set off an intense 14-hour manhunt that ended when 21-year-old Dylann Roof was arrested in a traffic stop about 220 miles (350 km) north of Charleston, South Carolina, where the shooting occurred, officials said.

Wednesday's mass shooting at the almost 200-year-old Emanuel African Methodist Episcopal Church, comes after a year of turmoil and protests over race relations, policing and criminal justice in the United States. A series of police killings of unarmed black men has sparked a renewed civil rights movement under the "Black Lives Matter" banner.

Four pastors, including Democratic state Senator Clementa Pinckney, 41, were among the six women and three men shot dead at the church nicknamed "Mother Emanuel," which was burned to the ground in the late 1820s after a slave revolt led by one of its founders.

"The fact that this took place in a black church obviously raises questions about a dark part of our history," said US President Barack Obama. "Once again, innocent people were killed in part because someone who wanted to inflict harm had no trouble getting their hands on a gun."

The United States has seen a series of mass shootings in recent years, including the 2012 massacre at Sandy Hook Elementary School, where a gunman killed 20 children and six adults. Democratic efforts to reform the nation's gun laws, protect by the Second Amendment of the US Constitution, failed after that incident.