'Not worried'
Starting from last month, the new sliding scale of 3p to 11p depends upon the value of what is up for sale.
The shop sellers have also seen a reduction in the visibility of their products to potential buyers.
Their goods now only appear if fewer than 30 items match a users' search criteria.
EBay hopes the change will stop potential buyers from getting swamped with too many available items.
The firm's UK community manager, Dan Wilson, said that while 100 traders were taking part in the boycott, this was a drop in the ocean compared to the tens of thousands of people registered as eBay shop sellers in the UK.
"We are not really seeing any tangible strike action and we are not that worried about it, although I don't want to dismiss the concerns of our customers," he said.
EBay has 15 million UK customers.
