Noca, an online payments start-up we wrote about last year, is officially launching its payment service today. Formed by ex-Visa employees, Noca originally offered a micro-payments system via two Facebook applications, OneClickPay and HelpYourWorld. The company is now offering payment services for unlimited amounts. Currently, Noca has two clients; digital content provider Klatcher.com and a local little league site. The advantage of Noca’s system is that it allows online merchants to bypass high transactional fees (usually 2-3 percent plus $0.30) imposed by credit card companies on consumer purchases.

Whether using Google Checkout, PayPal or Amazon Flexible Payment Service, merchants have been unable to avoid these fees, which can be pricey on expensive or luxury items. Until now. Noca’s online payment service only charges 0.25 percent on transactions and eliminated the fixed $0.30 fee all together. Once Noca’s system is enabled, the consumer’s issuing bank underwrites the risk so that the merchant receives payment within 1 to 2 business days.

On the consumer side, Noca assures security and prevention of identity theft because the transaction avoids credit cards and uses debit transactions instead, where the money goes directly from the buyer’s checking/savings account to the merchant. The user enters account and routing numbers into a virtual check, in a process which the company insists is secure. After entering routing and checking numbers, Noca will then send a text message with a code to the user’s cell phone, which needs to be inputed for the transaction to be completed.

With credit tight, consumers might feel more comfortable paying for items directly from a checking account. And it assures security for both merchants and consumers. Can Noca give PayPal a run for its money?