Mobile payments have usually been done via an app or third party add-on and only a few were targeted, said Mike Park, managing consultant of Trustwave. But with this type of payment functionality built into an entire platform, every device becomes a target, Park said via email.
When Apple Pay launches, researchers (and hackers) will immediately start looking for weaknesses, and there is little doubt they will find flaws, said Bob Doyle, a security consultant at Neohapsis, a security and risk management company.
"Everyone wants a thinner wallet. But the flipside of this is that it makes the mobile device so much more critical than it was before," Doyle said. "Even digital wallets will be picked."
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One possible security risk could stem from Apple's decision to place more trust in third party app developers, experts said.
Companies like Target, Uber and Groupon will incorporate Apple Pay into their e-commerce apps to facilitate purchases, which is another potential security risks, Pageler said.
According to Trustwave's Global Security Report, 96 percent of the applications scanned in 2013 contained at least one security vulnerability.
Apple executives also stressed during the event that the Touch ID feature found in the iPhone 5S and both models of the iPhone 6 could be used to verify payments, adding a layer of security. But since Touch ID launched in the iPhone 5S last year, there have already been experiments where the fingerprint reader was hacked.
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Also, given that people can access Apple Pay with an Apple Watch, which can be used with older models of the iPhone that do not have Touch ID, the fingerprint security feature is not necessary to use the payment service.
"It's still to early to tell where there are security weaknesses," Doyle said. "The devil is always in the details. Until we see the protocols we don't know what the vulnerabilities are."
Apple declined to comment.
—By CNBC's Cadie Thompson