NBC Universal revealed today why it prefers to use Microsoft’s Zune Marketplace for digital distribution over Apple’s iTunes. The reason may bring crippling security to Microsoft’s Zune portable media player and help Apple sell more iPods.

J.B. Perrette, NBC Universal president of digital distribution, shared that the organization had two primary issues with Apple that forced NBC to look towards Microsoft. The first is a typical answer coming from a studio - NBC wanted total control over pricing of its products while Apple wanted a one price for all scheme. The second, Apple refused to develop copyright filters into its iPod to remove pirated content. Microsoft bending to the will of NBC accepted both demands and will work on implement a filtering system on it’s devices.

Perrette explained NBC wanted “filtering technology that allows for playback of legitimately purchased content versus non-legitimately purchased content.” The system would be similar to what Google has been testing in its effort to block pirated clips from YouTube. Perrette also revealed NBC is current working with ISPs like AT&T to implement same ideas into their networks.

At least NBC realizes the potential impact of their heavy DRM tactics. “In the short term, this will not win us a lot of friends,” said Perrette. “In the long term, the consumer wants there to be quality premium-produced content, and in order for that to continue to be a viable business, there needs to be significant protection around it.”

Microsoft said the company was “sympathetic” to the situation, but declined to comment on the collaborative efforts or the possibility of crippling the Zune with piracy filters.

Apple currently has an overwhelming share of the portable media player market. So it is hard to imagine Microsoft adding such heavy DRM management capabilities to a Zune player that struggles to get what market share it can.