The Deluxe Diner's confederate flag will fly no more after its "naive" owner realised it was not a Dukes of Hazzard symbol.

On Wednesday, owner Chere Bailey threw the banner in the bin having learnt of its origin after the murder of nine black churchgoers in Charleston.

Bailey said she was completely against racism and slavery and did not want her diner to be associated with it, or the flag, which was emblazoned with the words "I ain't coming down".

Fairfax NZ Deluxe Diner owner Chere Bailey has removed a Confederate flag from the restaurant after learning about its sinister connotations.

"But it is coming down," she said. "I actually feel quite sick about it, I'm very sorry we were naive. I'm dead against racism and slavery and it's not something we want to be part of."

The flag was given to Bailey by a customer who said "you can't have a diner without one of these."

"He said it was controversial, but I thought it was just another state flag," she said.

"The only thing I knew about it was from the Dukes of Hazzard. I didn't realise it ran deeper than that."

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The Confederate flag was the battle flag of the rebelling Southern states in the US Civil war. It remained a symbol of southern pride and remembrance of the Confederate soldiers who died.

Over the years the flag has come to be a symbol for white supremacy groups and the accused Charleston shooter Dylann Roof, 21, posted photos with the flag on his website.

It's alleged Roof sat in on a bible study at the Emanuel African Methodist Episcopal Church before telling those gathered "you are raping our women and taking over our country," and then shooting nine people dead with a .45-calibre handgun.

Prompted by the shootings, protesters across the United States have called for the removal of the flag and on Tuesday South Carolina law makers began the process of considering the removal of the flag from the Capitol grounds.

Politicians in Virginia were looking at ways to remove the flag from licence plates and in Mississippi there were moves take the banner off the state's flag.

Campaigns against Confederate symbols had also risen in Texas, Tennessee and Columbia.

Democratic presidential contender Hillary Clinton even called for the removal of Confederate flags from public places across the United States and praised a number of businesses, including al-Mart, Amazon, eBay and Sears, who announced they would not sell products that featured the flag.

Bailey said she had lived in South Carolina and had witnessed racism first hand while working on a plantation near Charleston.

"There was a lot of racism in the hotel and I'd have big arguments with people, I couldn't understand the mentality. I'd say it's your choice you can change your view."

"The gardeners and maids were always black and in the streets you would never see white people cleaning. We worked in the gardens and things and when people drove passed they'd give us really horrible looks."

Online commentary was varied and while some comments were critical of Bailey's naivety, most supported her in taking the flag down.