The offending bit came during last week's "Jersey Shore" reunion special, when Mike "The Situation" Sorrentino flirts with an unidentified nightclub patron described by his friends as a "tranny."
GLAAD (the Gay & Lesbian Alliance Against Defamation) cried foul over the politically incorrect characterization.
"This was one of the most blatantly transphobic scenes aired anywhere on television in the last few years," the group said in a statement.
MTV will pull the segment after the current rotation cycle.
"We appreciate GLAAD voicing concern about the 'Jersey Shore' reunion special," the network said. "The segment in question was certainly not meant to be insensitive, but in retrospect we realize that it was offensive to some viewers. We sincerely apologize."