The shooting of nine black people at the Charleston Emanuel AME church in an evident racist attack has reignited controversy in the US about the use of the Confederate flag.

The man accused of the murders, Dylann Roof, had posed with the flag in photos posted online. It is associated with white supremacists who identify with the slave-holding southern states in the American Civil War. Opponents of flying the flag on official buildings consider it an emblem of slavery that has become a rallying symbol for racism and xenophobia in the United States.

Supporters, who fly the flag at their homes, wear it on clothing and put it on bumper stickers, see it is a symbol of the South's history and culture, as well a memorial to the roughly 480,000 Confederate casualties during the 1861-65 Civil War. That figure includes the dead, wounded and prisoners.

In a widely shared blog post, Russell Moore, president of the Ethics and Religious Liberty Commission of the Southern Baptist Convention, said that even as the descendant of Confederate veterans, the battle flag "makes me wince" because of its associations with slavery. "The Confederate States of America was not simply about limited government and local autonomy; the Confederate States of America was constitutionally committed to the continuation, with protections of law, [of] a great evil."

He said: "The Confederate Battle Flag may mean many things, but with those things it represents a defiance against abolition and against civil rights. The symbol was used to enslave the little brothers and sisters of Jesus, to bomb little girls in church buildings, to terrorize preachers of the gospel and their families with burning crosses on front lawns by night.

"That sort of symbolism is out of step with the justice of Jesus Christ. The cross and the Confederate flag cannot co-exist without one setting the other on fire."

While Moore's words were warmly praised by some including Danny Akin, president of Southeastern Baptist Theological Seminary, who tweeted his support, they are less likely to carry conviction in areas where loyalty to the historic South runs deep.

However, in a sign that the official line is shifting, South Carolina Governor Nikki Haley on Monday called on lawmakers to take down the at the state capitol grounds.

"It's time to move the flag from the capitol grounds," Haley, a Republican, told a news conference in the state capital, about 100 miles (161 km) from the Charleston shooting.

"The flag, while an integral part of our past, does not represent the future of our great state."

Haley called on lawmakers, whose normal legislative year wraps up this week, to address the issue over the summer and said she would order a special session if they did not.

The shooting at Emanuel African Methodist Episcopal Church came in a year of intense debate over US race relations following the killings of unarmed black men by police officers, which has sparked a reinvigorated civil rights movement under the "Black Lives Matter" banner.

Wal-Mart Stores Inc, the biggest US retailer, said it is pulling all Confederate flag merchandise from its stores.

"We never want to offend anyone with the products that we offer," spokesman Brian Nick said in a statement.

Sears Holding Corp said it would remove Confederate flags being sold by third parties on its website.

US senators Tim Scott and Lindsey Graham also urged removal of the flag. Both are Republicans and Graham is seeking the party's presidential nomination.

Among other Republicans, senators Lamar Alexander and Bob Corker of Tennessee also called for the removal of the flag. Mississippi House Speaker Philip Gunn said on Twitter that the Confederate emblem in his state's flag had to go.

A group of both black and white leaders called for a rally Tuesday at the State House to bring their demand to lawmakers.

"The only flag we should be worried about is the US flag," said Carl Smith, a 29-year-old black man, standing outside the church that was the site of the shooting. "Why would you support a flag that represents division instead of a flag that unites people?"

Roof was arrested on Thursday and charged with nine counts of murder for allegedly gunning down members of a Bible study group at the "Mother Emanuel" church. He is the apparent author of an online racist manifesto.

'NOT CURED' OF RACISM

President Barack Obama in a podcast posted online on Monday, said the killings showed the United States still had a long way to go in addressing racism, using an epithet to make his point.

"We're not cured of it," Obama told Marc Maron, host of the "WTF" podcast. "And it's not just a matter of it not being polite to say 'n___r' in public. That's not the measure of whether racism still exists."

Obama will deliver the eulogy at Friday's funeral of Reverend Clementa Pinckney, a state senator and pastor of the historic church, who was one of the nine people killed on Wednesday.

The debate is not a new one for South Carolina, which raised the flag over the State House in the early 1960s. The flag was moved to its current location, on a lower flagpole on the capitol grounds in 2000, a compromise at a time when some were calling for it to be retired.

A spokesman for the Sons of Confederate Veterans, a group that honours southern Civil War soldiers, called the move premature.

"This is the very worst possible time to be considering historic changes," said Ben Jones, the group's spokesman and a former US Representative from Georgia.

"Slavery, it ain't like it was a Southern sin," Jones said. "It was a national American sin. It built Wall Street and the American economy."

Earlier, South Carolina political and religious leaders called for action on the flag at a press conference in North Charleston, South Carolina, where a former police officer was charged with murdering a black civilian by shooting him in the back after he fled a traffic stop.

Several speakers said the flag's presence at the state's capital sent an unappealing message about South Carolina.

"Ridding the flag from the front of the State House is a start," said state Senator Marlon Kimpson, who is black.