The number of those killed in the Holocaust that is widely accepted is six million.
The Vatican has ordered Williamson to retract his comments. The British-born bishop responded that he needed more time to review the evidence.
Argentina's government said that Williamson's views were anti-Semitic and "deeply offended Argentine society".
Argentina is home to one of the world's largest Jewish communities outside of Israel.
The Reuter's news agency reported clergymen at the Buenos Aires seminary as saying Williamson had already left the compound.
Williamson belongs to the ultra-traditional Society of Saint Pius X.
Last month, Pope Benedict, the head of the Roman Catholic church, angered Jewish leaders and many Catholics by lifting the excommunication of Williamson and three others in a bid to heal a 20-year-old schism within the Church.
The schism began in 1988 when the four were ordained without Vatican permission.
World Jewish organisations and Angela Merkel, the German chancellor, criticised the pope for rehabilitating Williamson.
The pope, who is German-born, has tried to heal wounds by meeting Jewish leaders and ordering Williamson to recant his views.
Holocaust denial is a crime in Germany and state prosecutors in the southern city of Regensburg are investigating Williamson for incitement.
German neo-Nazi websites and blogs have published pieces supporting Williamson's stand.