The office of Muhammad Mahdi Akif, the "general guide" of the Islamist opposition group, said in a statement on Saturday that his remark on Thursday was meant merely to make a point about the West's attitude towards democracy and the Palestinians.
In a message on Thursday, Akif said: "Western democracy has attacked everyone who does not share the vision of the sons of Zion as far as the myth of the Holocaust is concerned."
He cited as evidence of Western intolerance the cases of Roger Garaudy, the French writer who was convicted of questioning the Holocaust in France in 1998, and David Irving, the British historian who faces similar charges in Austria next month.
But on Saturday, his office said: "Some media gave this a meaning which he [Akif] did not intend [and read it as] a denial that the Holocaust of the Jews by the Nazis during World War Two happened. The fact is that he did not deny that it took place."
West's double standards
"He [Akif] brought up the case of Garaudy ... to contrast it with the West's disregard for the victims of the Zionist state and its daily crimes against the Palestinians.
"He cited that as evidence of the West's policy of a double standard and of the democracy of exclusion which it practises on a wide scale."
About 6 million Jews are said to have been killed by the Nazis and their allies between 1933 and 1945.
The Muslim Brotherhood won 88 of the Egyptian parliament's 454 seats in elections in November and December, making the Brotherhood the largest opposition group in the chamber.