The competent court in Regensburg, southern Germany, must now decide whether to accept the charges, its president, Johann Ploed, said, adding that the decision would come in around one week.
Any punishment would likely be a fine, he said today.
If Biship Williamson accepted the fine, there would be no need for a public trial.
Bishop Williamson sparked controversy in January when he gave a television interview in the vicinity of Regensburg in which he said: "There was not one Jew killed by the gas chambers. It was all lies, lies, lies."
The bishop said he believed "200,000 to 300,000 Jews perished in Nazi concentration camps, but none of them by gas chambers".
The outburst prompted a very rare comment on religious matters by German Chancellor Angela Merkel, who called on Pope Benedict XVI to "clarify unambiguously that there can be no denial" the Nazis killed six million Jews.
The scandal carried particular resonance as it was Nazi Germany that masterminded and carried out the murders during World War II, and because the 82-year-old pope is German.
Denying that the Holocaust took place is illegal in Germany and Austria.
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