According to Chen's analysis, the price increases could have a 2 to 3 cent negative impact on Costco's fourth-quarter earnings per share, depending on the rate increase.
At Macy's and Nordstrom he estimates a 2 cent hit; at Target and Wal-Mart, a loss of 1 cent per share; and at Kohl's, between a zero and 1 cent per share decline. He added that the increases could also be a concern for Restoration Hardware, whose online sales account for half its business.
Though these dips would not drastically change retailers' holiday results, they highlight one of the frequent criticisms of the rise in online shopping.
Read More5 ways bigger online sales can hurt retailers
Although analysts acknowledge that Web investments are essential to staying relevant with consumers, it doesn't always mean they will see an increase in sales. It does, however, cause their margins to suffer—particularly as consumers have come to expect that retailers will eat the shipping costs.
According to a recent survey by comScore and UPS, 77 percent of online shoppers said free shipping is the most important criteria during checkout.
Read MoreAmazon sees Wal-Mart's bet, raises ante
Regarding the Journal report, UPS spokeswoman Susan Rosenberg said, "UPS approaches each customer's account to meet that customer's needs while also ensuring UPS is appropriately compensated for the valuable services we provide. We consider discussions with our customers regarding their service agreements as confidential."
Forrester Research predicts online retail sales will increase 12 percent in 2015 to $334 billion. That figure would represent 10 percent of all retail sales, according to the firm.