If President-elect Obama’s nominee to head the Federal Communications Commission is looking for an opportunity to begin more closely regulating network neutrality, he certainly has it at his disposal.

In a sternly worded letter, the FCC challenged Comcast, the U.S. largest cable operator, to prove that it is not blatantly giving preferential treatment to its own IP voice service over rivals such as Vonage.

The letter which was published by the FCC late Sunday is the latest installment in a long running legal war between Comcast and two policy watchdog groups.

The groups, Free Press and Public Knowledge, complained to the FCC that Comcast impedes network performance of independent companies such as VoIP firms that generate traffic on Comcast’s network.

The groups charge that Comcast is violating FCC rules by throttling the performance of rivals while giving network preference to its own competing applications. (Startups Battle Comcast Over Video Blocking)

In February 2008 Comcast filed a rebuttal saying that it manages traffic on its network so that its users don’t experience service degradation. (Comcast Sues FCC)

Comcast said that it does not discriminate against any particular class of content providers. All service providers are treated equally.

In its letter the FCC calls on Comcast to explain a discrepancy in its own advertising which says the Comcast’s VoIP service is not subject to the network management which governs its rivals.

Giving its VoIP service an unfettered free pass while subjecting rival services to possible performance degradation due to traffic management adjustments goes against FCC regulations.

Comcast has until January 30 to explain the discrepancy.

Network neutrality, a broad fairness theory that says carriers should not create separate performance tiers for certain streams of traffic over others, has been a hot button issue for more than three years.

At least two network neutrality bills have died in Congress because Democrats and Republicans generally come down on opposite sides of the issue.

Free market Republicans do not see a need for separate network neutrality regulation, preferring instead to allow market forces to settle the issue. Democrats generally favor network neutrality regulation.

But with a larger Democrat majority in Congress, and a new FCC chairman/nominee Julius Genachowski taking charge in Washington DC, many expect network neutrality regulation to receive a more favorable hearing on Capitol Hill. (Obama to Name Former VC to Head FCC)

And the Comcast wrangle seems like a good place for Mr. Genachowski, the first Democrat to head a Democrat-controlled FCC in eight years, to enter the discussion.