It's been a nerve-racking week for Amazon.com sellers after the e-retailer implemented new rules requiring merchants to supply dozens of invoices and pay a fee to sell certain big brands on the site.

Amazon is now trying to provide some clarity on what's known as "brand gating."

The Seattle-based company is telling existing sellers that they're being grandfathered into the system and that the charges, which typically range from $1,000 to $1,500 per brand, only apply to new merchants. In other words, if you've been selling Nike shoes or Hasbro toys for several years, it's business as usual.

Here's what Amazon spokesman Erik Fairleigh said in an e-mailed statement to CNBC.com:

"If a seller is already selling brands on Amazon that are now subject to a fee, they are not required to pay the fee to continue selling those brands. The fee only applies to new sellers of particular brands. Sellers can see whether a product requires a fee to sell when they search for that product using the "Add a Product" tool on Seller Central."

With the holiday season just around the corner, sellers that count on Amazon for the bulk of their revenue are on edge. Amazon has been hit with a swarm of counterfeiting, largely from Chinese manufacturers, in the past couple years, and is now responding with a heavy hand to get the problem under control.

By forcing brand resellers to show that their products are coming from legitimate sources, the thinking goes, Amazon can get rid of the bad actors and clean up the site. The third-party marketplace now accounts for close to half of e-commerce sales.

But the way Amazon has communicated this message to sellers has left plenty to be desired. Many merchants discovered the change late last week when they tried to upload a product listing only to find they were blocked unless they could provide invoices showing the purchase of at least 30 products over the previous 90 days. After clearing that hurdle, they'd have to remit a payment to get authorized.