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Customers love banking online, but not paying bills on the Web.

Banks have been ultra-aggressive in pushing customers toward electronic banking, urging them to pay their bills online. But if the numbers reflect anything, it’s that there’s more work to do before consumers feel comfortable about paying bills online — at least via their banks.

The good news for banks is that, for the first time ever, a clear majority of bank users want to use online banking. According to an April study released by J.D. Power and Associates, 51% of those customers surveyed said they preferred online banking, up from 45% in 2008.

This mirrors a more recent study by Mintel Comperemedia, which found that 70% of U.S. adults using the Internet also are online bankers. Another 7% of survey respondents said they’d actually signed up for online banking, but just haven’t used it yet.

Despite the number of those in favor of online banking in the Mintel study, roughly half of all online users didn’t want to use their online banking accounts to pay bills. Instead they bypass their banks, going straight to their billing vendors for payments such as utilities and cable.

The banks don’t want their customers doing such things. According to Online Banking Report, 80% of all online banking accounts don’t charge for their services. Yet some major banks do charge under certain conditions. Wells Fargo (Stock Quote: WFC), Netbank and Everbank all charge online bill pay fees if you don’t meet minimum account balance requirements.

Plus, in some cases, online bill payments are counted against a bank customer’s monthly transactions, which can trigger higher fees from crafty bankers. For instance, if your bank allows you 10 free transactions per month, a bevy of online bill payments can push your transactions above that number, incurring extra charges.

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Don’t worry, the banks aren’t taking this lying down. According to Mintel, about 40% of all bank direct mail offers mention online banking services.

“Despite the high penetration, banks are still eager to increase the usage of online banking,” says Susan Wolfe, vice president of financial services at Mintel Comperemedia. “It’s no secret that online banking creates deeper relationships between banks and customers, so banks are keen to pull in more users.”

If there’s money to be made, you can bet the banks will pull out all the stops to convince customers to pay their bills online — using the banks as middlemen.

What do bank customers use online banking services to accomplish?

  • Check balances: 93%
  • Receive account alerts: 38%
  • Pay their mortgages or credit cards issued by their banks: 30%

Source: Mintel Comperemedia

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