The move Monday by Walmart, the world's largest retailer and a staple in the south, came on the heels of a call by the governor of South Carolina for the contentious Civil War battle flag to be removed from its state house grounds.
The Confederate flag is seen as a symbol of racial violence and oppression by many, while some southerners romanticise it as a link to the historical south.
Civil rights activists have long pushed for it to be removed from official use, and the debate around it has returned to the spotlight since last week's massacre in Charleston, which left nine people dead at the hands of an alleged white supremacist who was seen in pictures with the banner.
"We never want to offend anyone with the products that we offer," Walmart spokesman Brian Nick said in a statement.
As of early Tuesday morning, searches for "Confederate flag" no longer returned flag results on Walmart's website.
"We have taken steps to remove all items promoting the Confederate flag from our assortment - whether in our stores or on our web site.
"We have a process in place to help lead us to the right decisions when it comes to the merchandise we sell. Still, at times, items make their way into our assortment improperly - this is one of those instances," he added.
South Carolina's Republican Governor Nikki Haley led growing bipartisan calls Monday for the removal of the flag from the grounds of the state capitol after the Charleston shooting.
A website apparently created by accused gunman Dylann Roof, 21, includes a racist screed and photographs of him holding a Confederate flag and a handgun.
Roof has been charged with nine murders over the 17 June rampage at the historic Emanuel African Methodist Episcopal Church in Charleston during a Bible study class.
His arrest warrant revealed how he allegedly shot the six women and three men, aged 26 through 87, multiple times with a high-caliber handgun and then stood over a survivor to make a "racially inflammatory" statement.
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