Emma Louise Morton's lawyer, Gavin Mansfield, entered the pleas to 49 charges on her behalf in the ACT Magistrates Court on Friday.

Mr Mansfield also successfully applied to vary the 47-year-old Campbell woman's bail conditions, allowing her to take part in Fair Work Commission proceedings against her former employer.

Ms Morton was arrested during a police raid in February and charged with 23 counts of obtaining property by deception, with a further 26 counts added last month.

She spent nearly two weeks in custody before being granted bail.

In documents previously tendered to the court, police said Ms Morton had been a director of the Weston Creek Children's Centre for about 22 years, managing up to 35 staff and overseeing the care of about 115 children per day.

The documents alleged that during the course of her employment, Ms Morton illegitimately transferred more than $160,000 from the centre's coffers to her personal bank accounts.

Investigators claimed the payments were "disguised" with descriptions falsely indicating they were for things like educational resources, tax payments and legal fees.

The documents also said Ms Morton moved $130,000 to unknown destinations, telling an admin manager the funds had gone to a "COVID account" and a term deposit.

They further alleged she made significant personal purchases, including a $3000 sofa seized by police from her home, using a debit card linked to a centre bank account.

At the time of Ms Morton's arrest, police said they suspected more than $480,000 had been misappropriated from the childcare centre.

To date, however, the amounts specified in charges laid against the 47-year-old add up to a smaller total that exceeds $330,000.

Ms Morton is due to return to court on June 24.

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