The network's Today programme has been accused of intentionally editing the 911 call to make it sound as if Zimmerman was making racist comments.
Neighbourhood watch member Zimmerman recently shot and killed 17-year-old Trayvon Martin in what he described as self-defence, meaning he has not been arrested for the incident, which has since sparked huge debate and controversy in the US.
Today aired a portion of the 911 clip, where Zimmerman says: "This guy looks like he's up to no good. He looks black."
However, the full call actually has Zimmerman stating: "This guy looks like he's up to no good, or he's on drugs or something. It's raining and he's just walking around, looking about."
The 911 operator replies: "Okay. And this guy, is he white, black or Hispanic?", to which Zimmerman responds: "He looks black."
"We have launched an internal investigation into the editorial process surrounding this particular story," a Today spokesman told The Hollywood Reporter.
Fox News's Sean Hannity has since played the Today clip, accusing the network of intentionally increasing racial tension.
20th Century Fox recently announced that it will be abandoning its marketing drive for upcoming comedy Neighbourhood Watch due to the tragedy.
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Watch Sean Hannity discuss the Today clip below: