eBay specifically bans their sale while Amazon bans the sale of "products that promote or glorify hatred, violence, racial, sexual or religious intolerance or promote organizations with such views."
It is difficult to enforce a complete ban on controversial products, analysts said, because of technological hurdles in flagging and pulling down banned items.
"For Amazon and eBay, it's a question of scale. eBay has had to work on everything from Nazi memorabilia to counterfeit jewelry and one of the hardest parts at their scale is to look at keywords, identify sellers with problems and flag issues," said Derek Bambauer, a professor at the University of Arizona who specializes in Internet law.
Amazon, which on Tuesday had listed nearly 30,000 items in a search for "Confederate flag", had almost nothing for sale with the flag late afternoon Wednesday.
Dylann Roof, the white 21-year-old charged with nine counts of murder in connection with the killings at a historically black church in South Carolina last week, posed with a Confederate flag in photos posted online.
The shooting has spawned a nationwide movement to eradicate symbols of the Confederacy from public spaces, license plates and retail stores, with both Wal-Mart Stores Inc and Sears Holdings Corp stopping sales.
ebay's Tuesday listing of 1,377 items had shrunk to 466.
The company said it uses a combination of automated and manual steps to flag and remove problematic listings, and it did not say why so many items remained.
Another challenge to keeping controversial products off the sites involves the guidelines the companies use. Despite its general ban on Nazi memorabilia, eBay list certain items from that era, which a representative said recognized the historical significance of World War II.
A search by Reuters found numerous coins and stamps from that era available for sale, including some bearing the image of Adolf Hitler or Nazi swastikas.
© Thomson Reuters 2015