FCC said 52 television ABC stations in the Central and Mountain zones had aired the scene at 9pm in violation of federal restrictions against broadcasting "obscene material" between 6am and 10pm.
The scene shows a young boy accidentally walking in on an older woman undressing in the bathroom. The FCC declared it indecent because it "depicts sexual organs and excretory organs -- specifically an adult woman's buttocks".
The FCC said that it received "numerous complaints" about the scene.
Stations in the Eastern and Pacific time zones were exempt because they broadcast the episode at 10pm local time.
ABC said that it opposes the fine and plans to appeal.
The network said that it had broadcast the episode and others from 'NYPD Blue', which ran from 1993 to 2005, with appropriate parental warnings and with V-chip enabled programme ratings when they were available.
ABC claimed that the writers of 'NYPD Blue' did not intend the scene to be titillating or lewd, but simply to reveal "the complexity and awkwardness involved when a single parent brings a new romantic partner into his or her life".
It added that the show had been on air for nearly a decade when the episode in question aired "and the realistic nature of its storylines was well known to the viewing public".
In 2006, CBS had to pay a $550,000 fine as a result of Janet Jackson's controversial "wardrobe malfunction", which exposed her right breast during the 2004 Super Bowl. CBS is appealing the fine.
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