The staff member at Capability Scotland at Upper Springland, Perth, was suspended while investigations are carried out.
The authorities have been informed while the company, which provides education, employment and care services for disabled children and adults, carry out an internal inquiry.
A spokeswoman for the charity said: "Capability Scotland have been made aware of an allegation against a member of staff at our Upper Springland service. This person has been suspended whilst we conduct a thorough investigation and we are working closely with the relevant authorities as we do so."
A Care Inspectorate spokesman said: "We have been notified of this incident and are satisfied the organisation has taken appropriate action to safeguard the welfare of service users."
Perth and Kinross Council said they had not been approached in respect of the investigation.