Brown, 27, formally entered the pleas in Melbourne Magistrates Court on Thursday afternoon while appearing on a videolink from prison.
The more than 150 charges relate to allegations of abusing children, bestiality, producing child abuse material, and contaminating food with intent to cause public alarm and anxiety.
Brown's defence barrister Rishi Nathwani KC told the court his client accepted a significant amount of the offending but there were still issues over which charges should proceed.
Mr Nathwani said discussions with prosecutors had been exhausted and the parties needed the assistance of the higher court.
"He will enter 'not guilty' pleas, which are really holding pleas in the circumstances," the barrister said.
When magistrate Donna Bakos asked Brown how he intended to plead to each of the charges, he responded twice, "not guilty, Your Honour".
She ordered Brown to face the Victorian County Court for a directions hearing in June.
He was remanded in custody after not making an application for bail.
Brown worked at 23 childcare centres across Melbourne between January 2017 and May 2025, Victoria Police say.
They included Creative Garden centre and Nino Early Learning Adventures, both located in Point Cook in Melbourne's southwest, and Aussie Kindies Early Learning Centre in Keilor.
Brown first faced court on May 12, 2025, for a filing hearing on more than 70 charges but the case was suppressed until police publicised the allegations on July 1.
Victorian authorities then advised the parents of about 2000 children who crossed paths with Brown to get them tested for infectious diseases.
A further 80 charges were laid in the subsequent months but prosecutors on Thursday withdrew six offences before the case was uplifted to the County Court.
Lifeline 13 11 14
Kids Helpline 1800 55 1800 (for people aged 5 to 25)
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028
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