The ease and speed of online business banking may be giving way to a growing amount of fraud. This month the Federal Bureau of Investigation warned about “a significant increase” in online banking frauds perpetrated on small and midsize businesses and local governments.

The FBI described a scenario in which a company's computer is infected when an employee–usually one with the authority to initiate funds transfers–clicks on an infected e-mail attachment or visits an infected Website. The malware installed on the computer harvests the logons for the company's bank accounts, and the cyber criminal uses that information to initiate ACH or wire transfers. An FBI report describing the problem estimates attempted thefts totaled about $100 million as of October.

Many small businesses aren't even aware of the threat to online banking until they're hit with a loss, says Avivah Litan, an analyst at technology research firm Gartner. And Litan notes that unlike consumers, who have legal protection in the case of such losses, businesses aren't necessarily able to recover money that is stolen from their accounts.