According to a report at the New York Post, “the Department of Justice and Federal Trade Commission are locked in negotiations over which of the watchdogs will begin an antitrust inquiry into Apple‘s new policy of requiring software developers who devise applications for devices such as the iPhone and iPad to use only Apple’s programming tools.”

Regulators are concerned that Apple “kills competition by forcing programmers to choose between developing apps that can run only on Apple gizmos or come up with apps that are platform neutral, and can be used on a variety of operating systems, such as those from rivals Google, Microsoft and Research In Motion,” says the Post.

Nonetheless, some say Apple’s restrictions are backfiring:

Shaun Meredith, a former Apple employee who runs software development company InfoBridge, said that as a result of Apple’s rule change, some of his customers are choosing to finance apps that are compatible with all of Apple’s competitors instead of those that work only with the iPhone or iPad.

Indeed, though Apple has the most applications, it is a distant second in terms of operating system market share. According to comScore, RIM, which makes the BlackBerry, has a 42 percent share, while Apple’s take is 25 percent. Microsoft has 15 percent and Google’s Android software has 9 percent.