Richard Williamson, from the ultra-conservative Saint Pius X Society, has denied the charges against him and refused to pay the €12,000 ($18,000) fine that would enable him to avoid trial, the spokesman said.
The court has not yet set a date for any potential trial and Williamson has the right not to appear in person but to appoint a lawyer to plead his case for him, the spokesman told AFP.
Williamson sparked an outcry in January when he gave an interview near Regensburg, southern Germany, in which he said that "not one Jew" was killed in gas chambers.
"It was all lies, lies, lies," he said in an interview that was later aired on Swedish television.
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, or questioning key elements, is illegal in Germany and Austria.