SAN FRANCISCO – Apple finds itself in unfamiliar territory: caught in the middle of a long-simmering conflict between retailers and credit card companies as it angles for consumers' mobile payments dollars, says CNET in a recent post.

That feud came to a head last week when pharmacy chains Rite Aid and CVS disabled consumers' ability to use Apple Pay, shortly after the new mobile payment system launched. Both Rite Aid and CVS belong to the Merchant Customer Exchange (MCX), a consortium of retailers that has developed its own mobile payments system as a way to bypass credit card fees. In contrast, Apple allied itself with leading credit card companies when it developed its Apple Pay mobile payments system.

At issue for both sides is which system consumers will prefer. On one hand, they have Apple Pay, which will allow consumers to make credit card purchases with one tap just by authenticating their fingerprints on an iPhone 6 or iPhone 6 Plus. Apple Pay works with a technology called near-field communication, or NFC, which allows the iPhone and the point-of-sale terminal to securely talk with each other over a short distance.

The MCX system, called CurrentC, relies on QR codes rather than fingerprint identification; it also lacks support for NFC and the tap-and-pay feature found on Apple Pay and Google Wallet, which uses the same technology. Additionally, CurrentC works with consumers’ bank accounts and gift cards rather than with credit cards. That's a big plus for merchants, when it comes to reducing the high swipe fees charged by credit card companies. But the biggest difference for merchants and consumers, according to CNET, may be that CurrentC will allow retailers to build loyalty programs, by tracking consumers' buying history and habits.

“It's all about loyalty. It's not about the new technology, not about the whiz bang factor,” David Robertson, an analyst with The Nilson Report, told CNET. “If you're the merchants, you are looking at 'how am I going to keep my head above water?”

The two formats are likely to duke it out in the marketplace, and time will tell which system is more readily adopted by consumers — and in turn, retailers. Right now, MCX has about 110,000 stores among its members (including Walmart, a leader of the organization), while Apple has claimed more than 220,000 stores in the Apple Pay network.