TV regulator Ofcom, Channel 4 and the Jewish Board of Deputies all received complaints about the song, which appeared on last Friday's programme.
The fictional Kazakh character Borat was shown singing a song called 'Throw the Jew Down the Well' in a country and western style to a crowded bar in mid-western America.
He began: "In my country there is a problem, and that problem is the Jew, they take everybody money and don't give it back."
The chorus used the words: "Throw the Jew down the well so my country can be free. You must grab him by the horns, then we have a big party."
The Americans in the bar were shown singing along happily with Baron Cohen.
However, Baron Cohen is Jewish and the song was intended to be tongue in cheek.
A Channel 4 spokesman said: "Sacha Baron Cohen's humour is ironic and actually highlights bigotry and ignorance."
The second and final part of 'Borat's Television Programme' is to be shown on Channel 4 tonight at 9.30pm. A sketch showing an anti-Semitic Texan gamehunter is likely to cause similar outrage.
Ofcom has so far received six viewer complaints about the programme and will decide whether to penalise the programme's production company or Channel 4 later this year.
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