Cardinal Pell, who is considered the Church's third-ranked official, took a leave of absence from the Vatican past year to fight the charges in his home country.
Some charges were earlier withdrawn by prosecutors. "The whole idea of sexual abuse is abhorrent to me".
Wallington also struck out another charge centred on an incident at a swimming pool after she found the complainant was an "unsatisfactory witness".
The trial against Pell began after the cardinal testified on three occasions as a witness before the Royal Commission which investigated Australia's public and religious institutions and their involvement in alleged sexual abuse against minors.
A statement said the Holy See had "taken note" of the ruling.
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Magistrate Belinda Wallington will rule in the Melbourne Magistrates Court on whether the prosecution's case against Pell is strong enough to warrant a trial by jury. A further related charge was withdrawn. The nature of those allegations can not be detailed for legal reasons.
"It's in the hands of the justice system and one can not judge before the justice system", he said.
Corrects Pell was seated, not standing, when he entered his plea.
Pell has vehemently denied the claims, calling them "utterly false", and his defence barrister has already made clear Pell will plead not guilty at any future trial.
The small print of the allegations have but to be launched to the general public, although police have described the fees as "historic" sexual assault offences.
Flanked by up to 40 police officers, Cardinal Pell had arrived at the court in a white sedan just after 9am.
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Pell did not comment when he left the court, surrounded by police and flanked by his legal team.
She didn't specify which prices will likely be proceed to court docket or any additional element on the date of the trial.
"No matter what happens from here ... it is not going to be easy".
A statement released on behalf of Pell through law firm Galbally and O'Bryan on Tuesday afternoon said Pell would like to thank his supporters for their "continuing support and prayers".
"He will defend the remaining charges".
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Find the direct link to JEE Main Result 2018 at the top of this page / here then provide and the details in the form. (G.N.S) DT.30 The results of IIT-JEE (Mains) examination will most likely be declared today, April 30.