She was charged on Thursday with one count of stealing as a servant.
The first-term councillor allegedly redirected client invoices and unauthorised refunds to her own accounts.
The charges came after a five-month investigation by the Queensland Police Service's Fraud and Cyber Crime Group.
A Logan City Council spokeswoman said the Queensland Police Service had notified the council of"charges relating to fraud,against a current councillor"and Cr McIntosh had been stood down from her position.
"Logan City Council has strict and transparent policies governing financial transactions and councillor conduct,"she said.
"While the councillor is entitled to the presumption of innocence,in the matter of public interest,the councillor has been requested to stand down from participating in council matters and the councillor has agreed.
"As the former councillor for Division 6,mayor Luke Smith will immediately oversee the duties of this division until the new year and more permanent arrangements are in place."