Emma Louise Morton, 46, was arrested during a police raid on her Campbell home before appearing by video in the ACT Magistrates Court on a lengthy list of charges.

Police allege that over a period of months Ms Morton transferred tens of thousands of dollars from the Weston Creek Children's Centre to her own accounts.

The court heard there was a total of nearly $500,000 missing from the centre's accounts and further charges were likely.

Documents tendered to the court say Ms Morton disguised the payments by labelling them with descriptors such as "Cleaning" or "Modern Teaching Aids".

She allegedly explained one transfer of $50,000 as being suggested by the bank to another account they were calling the COVID account.

Police also allege Ms Morton used the centre's Visa card while staying at the Hotel Realm in August last year following the breakup of her marriage.

A staff member noticed the charges and flagged them with a board member, who then raised them with Ms Morton.

But the director later resigned and there was no one left to oversee Ms Morton's activities, the documents allege.

She had been in the role of centre director for 22 years.

Lawyer Taden Kelliher applied for Ms Morton's release on bail, saying she had strong ties to the territory.

But prosecutor Kiara Sheridan opposed her release, pointing to fears she would interfere with the evidence or commit further offences.

Magistrate Glenn Theakston said the "amounts are staggering" as he refused Ms Morton bail on the allegations.

Mr Theakston said he was not refusing bail for good but for the immediate future while police worked to find the missing money.

Ms Morton put her head into her hands and broke down on hearing the magistrate's decision.

She is charged with 23 counts of fraud allegedly committed between July 2020 to February 2021. She did not enter any pleas.

Police have frozen several of her bank accounts.

In a statement, police said the safety of children at the centre had not been compromised as a result of the alleged fraud.

Police said they would speak with the government to ensure the centre could stay open.

Ms Morton will return to court at a later date.

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